Methods and compositions for modulating a genome

ABSTRACT

The disclosure provides, e.g., compositions, systems, and methods for targeting, editing, modifying, or manipulating a host cell&#39;s genome at one or more locations in a DNA sequence in a cell, tissue, or subject.

RELATED APPLICATIONS

This application is a continuation of U.S. Ser. No. 18/356,013, filed Jul. 20, 2023, which is a continuation of International Application No. PCT/US2022/076045, filed Sep. 7, 2022, which claims priority to U.S. Ser. No. 63/241,953, filed Sep. 8, 2021 and 63/373,444, filed Aug. 24, 2022, the entire contents of each of which is incorporated herein by reference.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has been submitted electronically in XML format and is hereby incorporated by reference in its entirety. Said XML copy, created on Aug. 8, 2023, is named V2065-702322FT_SL.xml and is 20,090,558 bytes in size.

BACKGROUND

Integration of a nucleic acid of interest into a genome occurs at low frequency and with little site specificity, in the absence of a specialized protein to promote the insertion event. Some existing approaches, like CRISPR/Cas9, are more suited for small edits that rely on host repair pathways, and are less effective at integrating longer sequences. Other existing approaches, like Cre/loxP, require a first step of inserting a loxP site into the genome and then a second step of inserting a sequence of interest into the loxP site. There is a need in the art for improved compositions (e.g., proteins and nucleic acids) and methods for inserting, altering, or deleting sequences of interest in a genome.

SUMMARY OF THE INVENTION

This disclosure relates to novel compositions, systems and methods for altering a genome at one or more locations in a host cell, tissue or subject, in vivo or in vitro. In particular, the invention features compositions, systems and methods for inserting, altering, or deleting sequences of interest in a host genome.

Features of the compositions or methods can include one or more of the following enumerated embodiments.

-   -   1. A gene modifying polypeptide comprising:         -   a DNA binding domain (DBD) that binds to a target nucleic             acid sequence and         -   a reverse transcriptase (RT) domain of Table 1, or a             sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 97%,             98%, or 99% identity thereto (e.g., to a sequence as listed             for the RT domain in Table 6);         -   wherein the DBD is heterologous to the RT domain (e.g., a             Cas domain, e.g., a Cas nickase domain, e.g., a Cas9 nickase             domain); optionally wherein the RT domain is C-terminal of             the Cas domain; and         -   a linker disposed between the RT domain and the Cas domain,             wherein the linker has a sequence from the same row of Table             1 as the RT domain, or a sequence having at least 70%, 75%,             80%, 85%, 90%, 95%, 97%, 98%, or 99% identity thereto.     -   2. The gene modifying polypeptide of embodiment 1, wherein the         RT domain has a sequence with at least 90% identity to the RT         domain of Table 1.     -   3. The gene modifying polypeptide of any of the preceding         embodiments, wherein the RT domain has a sequence with at least         95% identity to the RT domain of Table 1.     -   4. The gene modifying polypeptide of any of the preceding         embodiments, wherein the RT domain has a sequence with at least         98% identity to the RT domain of Table 1.     -   5. The gene modifying polypeptide of any of the preceding         embodiments, wherein the RT domain has a sequence with at least         99% identity to the RT domain of Table 1.     -   6. The gene modifying polypeptide of any of the preceding         embodiments, wherein the RT domain has a sequence with 100%         identity to the RT domain of Table 1.     -   7. The gene modifying polypeptide of any of the preceding         embodiments, wherein the linker has a sequence with at least 90%         identity to the linker sequence from the same row of Table 1 as         the RT domain.     -   8. The gene modifying polypeptide of any of the preceding         embodiments, wherein the linker has a sequence with at least 95%         identity to the linker sequence from the same row of Table 1 as         the RT domain.     -   9. The gene modifying polypeptide of any of the preceding         embodiments, wherein the linker has a sequence with at least 97%         identity to the linker sequence from the same row of Table 1 as         the RT domain.     -   10. The gene modifying polypeptide of any of the preceding         embodiments, wherein the linker has a sequence with 100%         identity to the linker sequence from the same row of Table 1 as         the RT domain.     -   11. The gene modifying polypeptide of any of the preceding         embodiments, wherein the RT domain comprises a mutation as         listed in Table 2.     -   12. The gene modifying polypeptide of any of the preceding         embodiments, wherein the Cas domain comprises a sequence of         Table 7 or 8, or a sequence having at least 70%, 75%, 80%, 85%,         90%, 95%, 98%, or 99% identity thereto.     -   13. The gene modifying polypeptide of any of the preceding         embodiments, wherein the Cas domain is a Cas nickase domain.     -   14. The gene modifying polypeptide of any of the preceding         embodiments, wherein the Cas domain is a Cas9 nickase domain.     -   15. The gene modifying polypeptide of any of the preceding         embodiments, wherein the Cas domain comprises an N863A mutation.     -   16. The gene modifying polypeptide of any of the preceding         embodiments, which comprises an NLS, e.g., wherein the gene         modifying polypeptide comprises two NLSs.     -   17. The gene modifying polypeptide of any of the preceding         embodiments, which comprises an NLS N-terminal of the Cas9         domain.     -   18. The gene modifying polypeptide of any of the preceding         embodiments, which comprises an NLS C-terminal of the RT domain.     -   19. The gene modifying polypeptide of any of the preceding         embodiments, which comprises a first NLS which is N-terminal of         the Cas9 domain and a second NLS which is C-terminal of the RT         domain.     -   20. The gene modifying polypeptide of any of the preceding         embodiments, which comprises a sequence of SEQ ID NO: 4000 which         comprises the first NLS and the Cas domain, or a sequence having         at least 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 99% identity         thereto.     -   21. The gene modifying polypeptide of any of the preceding         embodiments, which comprises a sequence of SEQ ID NO: 4001 which         comprises the second NLS, or a sequence having at least 70%,         75%, 80%, 85%, 90%, 95%, 98%, or 99% identity thereto.     -   22. The gene modifying polypeptide of any of the preceding         embodiments, which comprises a GG amino acid sequence between         the Cas domain and the linker.     -   23. The gene modifying polypeptide of any of the preceding         embodiments, which comprises an AG amino acid sequence between         the RT domain and the second NLS.     -   24. The gene modifying polypeptide of any of the preceding         embodiments, which comprises a GG amino acid sequence between         the linker and the RT domain.     -   25. The gene modifying polypeptide of any of the preceding         embodiments, which comprises an 20 amino acid sequence according         to any of SEQ ID NOs: 1-3332 in the sequence listing, or a         sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%,         or 99% identity thereto.     -   26. The gene modifying polypeptide of any of the preceding         embodiments, which comprises an amino acid sequence with at         least 90% identity to any of SEQ ID NOs: 1-3332 in the sequence         listing.     -   27. The gene modifying polypeptide of any of the preceding         embodiments, which comprises an amino acid sequence with at         least 95% identity to any of SEQ ID NOs: 1-3332 in the sequence         listing.     -   28. The gene modifying polypeptide of any of the preceding         embodiments, which comprises an amino acid sequence with at         least 98% identity to any of SEQ ID NOs: 1-3332 in the sequence         listing.     -   29. The gene modifying polypeptide of any of the preceding         embodiments, which comprises an amino acid sequence with at         least 99% identity to any of SEQ ID NOs: 1-3332 in the sequence         listing.     -   30. The gene modifying polypeptide of any of the preceding         embodiments, which comprises an amino acid sequence with 100%         identity to any of SEQ ID NOs: 1-3332 in the sequence listing.     -   31. The gene modifying polypeptide of any of the preceding         embodiments, which produces an increase in converted GFP+ of at         least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 75%, 80%, 85%, 90%,         95%, 100%, 125%, 150%, 175%, 200%, 250%, 300%, 400%, 500%, 600%,         700%, 800%, 900%, 1000%, 1500%, 2000%, or 2500% relative to         unsorted input cells in an assay of Example 2 using HEK cells         (e.g., HEK293T cells) and g4 guide RNA.     -   32. The gene modifying polypeptide of any of the preceding         embodiments, which produces an increase in converted GFP+ of at         least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 75%, 80%, 85%, 90%,         95%, 100%, 125%, 150%, 175%, 200%, 250%, 300%, 400%, 500%, 600%,         700%, 800%, 900%, 1000%, 1500%, 2000%, or 2500% relative to         unsorted input cells in an assay of Example 2 using U2-OS cells         and g4 guide RNA.     -   33. The gene modifying polypeptide of any of the preceding         embodiments, which produces an increase in converted GFP+ of at         least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 75%, 80%, 85%, 90%,         95%, 100%, 125%, 150%, 175%, 200%, 250%, 300%, 400%, 500%, 600%,         700%, 800%, 900%, 1000%, 1500%, 2000%, or 2500% relative to         unsorted input cells in an assay of Example 2 using HEK cells         (e.g., HEK293T cells) and g10 guide RNA.     -   34. The gene modifying polypeptide of any of the preceding         embodiments, which has an activity that is at least 50%, 60%,         70%, 80%, or 90% of the activity of a gene modifying polypeptide         comprising, in an N-terminal to C-terminal direction:         -   a) an NLS and Cas domain sequence of SEQ ID NO: 4000;         -   b) a linker having the sequence EAAAKGSS (SEQ ID NO: 5152);         -   c) an RT domain having the sequence of PERV_Q4VFZ2_3mutA_WS;             and         -   d) an NLS sequence of SEQ ID NO: 4001, in an assay of             Example 1 using HEK cells and g4 guide RNA.     -   35. The gene modifying polypeptide of any of the preceding         embodiments, which has an activity that is at least 10%, 20%,         30%, 40%, 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 125%,         150%, 175%, 200%, 250%, 300%, 400%, 500%, 600%, 700%, 800%,         900%, 1000%, 1500%, 2000%, or 2500% greater than the activity of         a gene modifying polypeptide comprising a sequence of SEQ ID NO:         4002 in an assay of Example 1, e.g., using HEK cells and g4         guide RNA.     -   36. A nucleic acid (e.g., DNA or RNA, e.g., mRNA) encoding the         gene modifying polypeptide of any of the preceding embodiments.     -   37. A cell comprising the gene modifying polypeptide of any of         embodiments 1-35 or the nucleic acid of embodiment 36.     -   38. A system comprising:         -   i) the gene modifying polypeptide of any of embodiments             1-35, and         -   ii) a template RNA that comprises:             -   a) a gRNA spacer that is complementary to a portion a                 target nucleic acid sequence;             -   b) a gRNA scaffold that binds the Cas domain of the gene                 modifying polypeptide;             -   c) a heterologous object sequence; and             -   d) a primer binding site sequence (PBS sequence).     -   39. A method for modifying a target nucleic acid in a cell         (e.g., a human cell), the method comprising contacting the cell         with the system of embodiment 38, or nucleic acid encoding the         same, thereby modifying the target nucleic acid.     -   40. A gene modifying polypeptide comprising:         -   a Cas domain (e.g., a Cas nickase domain, e.g., a Cas9             nickase domain);         -   a reverse transcriptase (RT) domain comprising the RT domain             of a reference gene modifying polypeptide having the             sequence of any one of SEQ ID NOs: 1-7743, or a sequence             having at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or             99% identity thereto, wherein the RT domain is C-terminal of             the Cas domain; and         -   a linker disposed between the RT domain and the Cas domain,             wherein the linker comprises the linker of said reference             gene modifying polypeptide, or a sequence having at least             70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% identity             thereto.     -   41. The gene modifying polypeptide of embodiment 40, wherein the         reference gene modifying polypeptide has the amino acid sequence         of a SEQ ID NO as listed in Table 1.     -   42. The gene modifying polypeptide of embodiment 40, wherein the         reference gene modifying polypeptide has the amino acid sequence         of a SEQ ID NO as listed in Table A1.     -   43. The gene modifying polypeptide of embodiment 40, wherein the         reference gene modifying polypeptide has the amino acid sequence         of a SEQ ID NO as listed in Table A5.     -   44. The gene modifying polypeptide of embodiment 40, wherein the         reference gene modifying polypeptide has the amino acid sequence         of a SEQ ID NO as listed in Table D1.     -   45. The gene modifying polypeptide of embodiment 40, wherein the         reference gene modifying polypeptide has the amino acid sequence         of a SEQ ID NO as listed in Table D2.     -   46. The gene modifying polypeptide of embodiment 40, wherein the         reference gene modifying polypeptide has the amino acid sequence         of a SEQ ID NO as listed in Table D3.     -   47. The gene modifying polypeptide of embodiment 40, wherein the         reference gene modifying polypeptide has the amino acid sequence         of a SEQ ID NO as listed in Table D4.     -   48. The gene modifying polypeptide of embodiment 40, wherein the         reference gene modifying polypeptide has the amino acid sequence         of a SEQ ID NO as listed in Table D5.     -   49. The gene modifying polypeptide of embodiment 40, wherein the         reference gene modifying polypeptide has the amino acid sequence         of a SEQ ID NO as listed in Table D6.     -   50. The gene modifying polypeptide of embodiment 40, wherein the         reference gene modifying polypeptide has the amino acid sequence         of a SEQ ID NO as listed in Table D7.     -   51. The gene modifying polypeptide of embodiment 40, wherein the         reference gene modifying polypeptide has the amino acid sequence         of a SEQ ID NO as listed in Table D8.     -   52. The gene modifying polypeptide of embodiment 40, wherein the         reference gene modifying polypeptide has the amino acid sequence         of a SEQ ID NO as listed in Table D9.     -   53. The gene modifying polypeptide of embodiment 40, wherein the         reference gene modifying polypeptide has the amino acid sequence         of a SEQ ID NO as listed in Table D10.     -   54. The gene modifying polypeptide of embodiment 40, wherein the         reference gene modifying polypeptide has the amino acid sequence         of a SEQ ID NO as listed in Table D11.     -   55. The gene modifying polypeptide of embodiment 40, wherein the         reference gene modifying polypeptide has the amino acid sequence         of a SEQ ID NO as listed in Table D12.     -   56. The gene modifying polypeptide of embodiment 40, wherein the         reference gene modifying polypeptide has the amino acid sequence         of a SEQ ID NO as listed in Table T1.     -   57. The gene modifying polypeptide of embodiment 40, wherein the         reference gene modifying polypeptide has the amino acid sequence         of a SEQ ID NO as listed in Table T2.     -   58. The gene modifying polypeptide of embodiment 40, wherein the         reference gene modifying polypeptide is an AVIRE polypeptide         (e.g., as described herein), and wherein the linker comprises an         amino acid sequence as listed in FIG. 11 .     -   59. A gene modifying polypeptide comprising:         -   a Cas domain (e.g., a Cas nickase domain, e.g., a Cas9             nickase domain);         -   a reverse transcriptase (RT) domain of Table 1, or a             sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 97%,             98%, or 99% identity thereto, wherein the RT domain is             C-terminal of the Cas domain; and         -   a linker disposed between the RT domain and the Cas domain,             wherein the linker has a sequence from the same row of Table             1 as the RT domain, or a sequence having at least 70%, 75%,             80%, 85%, 90%, 95%, 97%, 98%, or 99% identity thereto.     -   60. A gene modifying polypeptide comprising:         -   a Cas domain (e.g., a Cas nickase domain, e.g., a Cas9             nickase domain);         -   a reverse transcriptase (RT) domain of Table A1, or a             sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 97%,             98%, or 99% identity thereto, wherein the RT domain is             C-terminal of the Cas domain; and         -   a linker disposed between the RT domain and the Cas domain,             wherein the linker comprises a sequence from the same row of             Table A1 as the RT domain, or a sequence having at least             70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% identity             thereto.     -   61. A gene modifying polypeptide comprising:         -   a Cas domain (e.g., a Cas nickase domain, e.g., a Cas9             nickase domain);         -   a reverse transcriptase (RT) domain of Table A5, or a             sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 97%,             98%, or 99% identity thereto, wherein the RT domain is             C-terminal of the Cas domain; and         -   a linker disposed between the RT domain and the Cas domain,             wherein the linker comprises a sequence from the same row of             Table D1 as the RT domain, or a sequence having at least             70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% identity             thereto.     -   62. A gene modifying polypeptide comprising:         -   a Cas domain (e.g., a Cas nickase domain, e.g., a Cas9             nickase domain);         -   a reverse transcriptase (RT) domain of Table T1, or a             sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 97%,             98%, or 99% identity thereto, wherein the RT domain is             C-terminal of the Cas domain; and         -   a linker disposed between the RT domain and the Cas domain,             wherein the linker comprises a sequence from the same row of             Table D1 as the RT domain, or a sequence having at least             70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% identity             thereto.     -   63. A gene modifying polypeptide comprising:         -   a Cas domain (e.g., a Cas nickase domain, e.g., a Cas9             nickase domain);         -   a reverse transcriptase (RT) domain of Table T2, or a             sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 97%,             98%, or 99% identity thereto, wherein the RT domain is             C-terminal of the Cas domain; and         -   a linker disposed between the RT domain and the Cas domain,             wherein the linker comprises a sequence from the same row of             Table D1 as the RT domain, or a sequence having at least             70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% identity             thereto.     -   64. A gene modifying polypeptide comprising:         -   a Cas domain (e.g., a Cas nickase domain, e.g., a Cas9             nickase domain);         -   a reverse transcriptase (RT) domain of Table D1, or a             sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 97%,             98%, or 99% identity thereto, wherein the RT domain is             C-terminal of the Cas domain; and         -   a linker disposed between the RT domain and the Cas domain,             wherein the linker comprises a sequence from the same row of             Table D1 as the RT domain, or a sequence having at least             70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% identity             thereto.     -   65. A gene modifying polypeptide comprising:         -   a Cas domain (e.g., a Cas nickase domain, e.g., a Cas9             nickase domain);         -   a reverse transcriptase (RT) domain of Table D2, or a             sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 97%,             98%, or 99% identity thereto, wherein the RT domain is             C-terminal of the Cas domain; and         -   a linker disposed between the RT domain and the Cas domain,             wherein the linker comprises a sequence from the same row of             Table D2 as the RT domain, or a sequence having at least             70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% identity             thereto.     -   66. A gene modifying polypeptide comprising:         -   a Cas domain (e.g., a Cas nickase domain, e.g., a Cas9             nickase domain);         -   a reverse transcriptase (RT) domain of Table D3, or a             sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 97%,             98%, or 99% identity thereto, wherein the RT domain is             C-terminal of the Cas domain; and         -   a linker disposed between the RT domain and the Cas domain,             wherein the linker comprises a sequence from the same row of             Table D3 as the RT domain, or a sequence having at least             70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% identity             thereto.     -   67. A gene modifying polypeptide comprising:         -   a Cas domain (e.g., a Cas nickase domain, e.g., a Cas9             nickase domain);         -   a reverse transcriptase (RT) domain of Table D4, or a             sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 97%,             98%, or 99% identity thereto, wherein the RT domain is             C-terminal of the Cas domain; and         -   a linker disposed between the RT domain and the Cas domain,             wherein the linker comprises a sequence from the same row of             Table D4 as the RT domain, or a sequence having at least             70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% identity             thereto.     -   68. A gene modifying polypeptide comprising:         -   a Cas domain (e.g., a Cas nickase domain, e.g., a Cas9             nickase domain);         -   a reverse transcriptase (RT) domain of Table D5, or a             sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 97%,             98%, or 99% identity thereto, wherein the RT domain is             C-terminal of the Cas domain; and         -   a linker disposed between the RT domain and the Cas domain,             wherein the linker comprises a sequence from the same row of             Table D5 as the RT domain, or a sequence having at least             70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% identity             thereto.     -   69. A gene modifying polypeptide comprising:         -   a Cas domain (e.g., a Cas nickase domain, e.g., a Cas9             nickase domain);         -   a reverse transcriptase (RT) domain of Table D6, or a             sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 97%,             98%, or 99% identity thereto, wherein the RT domain is             C-terminal of the Cas domain; and         -   a linker disposed between the RT domain and the Cas domain,             wherein the linker comprises a sequence from the same row of             Table D6 as the RT domain, or a sequence having at least             70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% identity             thereto.     -   70. A gene modifying polypeptide comprising:         -   a Cas domain (e.g., a Cas nickase domain, e.g., a Cas9             nickase domain);         -   a reverse transcriptase (RT) domain of Table D7, or a             sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 97%,             98%, or 99% identity thereto, wherein the RT domain is             C-terminal of the Cas domain; and         -   a linker disposed between the RT domain and the Cas domain,             wherein the linker comprises a sequence from the same row of             Table D7 as the RT domain, or a sequence having at least             70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% identity             thereto.     -   71. A gene modifying polypeptide comprising:         -   a Cas domain (e.g., a Cas nickase domain, e.g., a Cas9             nickase domain);         -   a reverse transcriptase (RT) domain of Table D8, or a             sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 97%,             98%, or 99% identity thereto, wherein the RT domain is             C-terminal of the Cas domain; and         -   a linker disposed between the RT domain and the Cas domain,             wherein the linker comprises a sequence from the same row of             Table D8 as the RT domain, or a sequence having at least             70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% identity             thereto.     -   72. A gene modifying polypeptide comprising:         -   a Cas domain (e.g., a Cas nickase domain, e.g., a Cas9             nickase domain);         -   a reverse transcriptase (RT) domain of Table D9, or a             sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 97%,             98%, or 99% identity thereto, wherein the RT domain is             C-terminal of the Cas domain; and         -   a linker disposed between the RT domain and the Cas domain,             wherein the linker comprises a sequence from the same row of             Table D9 as the RT domain, or a sequence having at least             70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% identity             thereto.     -   73. A gene modifying polypeptide comprising:         -   a Cas domain (e.g., a Cas nickase domain, e.g., a Cas9             nickase domain);         -   a reverse transcriptase (RT) domain of Table D10, or a             sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 97%,             98%, or 99% identity thereto, wherein the RT domain is             C-terminal of the Cas domain; and         -   a linker disposed between the RT domain and the Cas domain,             wherein the linker comprises a sequence from the same row of             Table D10 as the RT domain, or a sequence having at least             70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% identity             thereto.     -   74. A gene modifying polypeptide comprising:         -   a Cas domain (e.g., a Cas nickase domain, e.g., a Cas9             nickase domain);         -   a reverse transcriptase (RT) domain of Table D11, or a             sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 97%,             98%, or 99% identity thereto, wherein the RT domain is             C-terminal of the Cas domain; and         -   a linker disposed between the RT domain and the Cas domain,             wherein the linker comprises a sequence from the same row of             Table D11 as the RT domain, or a sequence having at least             70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% identity             thereto.     -   75. A gene modifying polypeptide comprising:         -   a Cas domain (e.g., a Cas nickase domain, e.g., a Cas9             nickase domain);         -   a reverse transcriptase (RT) domain of Table D12, or a             sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 97%,             98%, or 99% identity thereto, wherein the RT domain is             C-terminal of the Cas domain; and         -   a linker disposed between the RT domain and the Cas domain,             wherein the linker comprises a sequence from the same row of             Table D12 as the RT domain, or a sequence having at least             70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% identity             thereto.     -   76. A gene modifying polypeptide comprising:         -   a Cas domain (e.g., a Cas nickase domain, e.g., a Cas9             nickase domain);         -   a reverse transcriptase (RT) domain of Table T1, or a             sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 97%,             98%, or 99% identity thereto, wherein the RT domain is             C-terminal of the Cas domain; and         -   a linker disposed between the RT domain and the Cas domain,             wherein the linker comprises a sequence from the same row of             Table T1 as the RT domain, or a sequence having at least             70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% identity             thereto.     -   77. A gene modifying polypeptide comprising:         -   a Cas domain (e.g., a Cas nickase domain, e.g., a Cas9             nickase domain);         -   a reverse transcriptase (RT) domain of Table T2, or a             sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 97%,             98%, or 99% identity thereto, wherein the RT domain is             C-terminal of the Cas domain; and         -   a linker disposed between the RT domain and the Cas domain,             wherein the linker comprises a sequence from the same row of             Table T2 as the RT domain, or a sequence having at least             70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% identity             thereto.     -   78. A gene modifying polypeptide comprising:         -   a Cas domain (e.g., a Cas nickase domain, e.g., a Cas9             nickase domain);         -   an AVIRE reverse transcriptase (RT) domain (e.g., as             described herein), or a sequence having at least 70%, 75%,             80%, 85%, 90%, 95%, 97%, 98%, or 99% identity thereto,             wherein the RT domain is C-terminal of the Cas domain; and         -   a linker disposed between the RT domain and the Cas domain,             wherein the linker comprises a sequence as listed in FIG. 11             , or a sequence having at least 70%, 75%, 80%, 85%, 90%,             95%, 97%, 98%, or 99% identity thereto.     -   79. The gene modifying polypeptide of any one of embodiments         1-78, wherein the RT domain comprises an amino acid sequence of         an AVIRE RT domain (e.g., as described in Table 6), or a         sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%,         99%, or 100% identity thereto.     -   80. The gene modifying polypeptide of any one of embodiments         1-78, wherein the RT domain comprises an amino acid sequence of         an BAEVM RT domain (e.g., as described in Table 6), or a         sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%,         99%, or 100% identity thereto.     -   81. The gene modifying polypeptide of any one of embodiments         1-78, wherein the RT domain comprises an amino acid sequence of         an FFV RT domain (e.g., as described in Table 6), or a sequence         having at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or         100% identity thereto.     -   82. The gene modifying polypeptide of any one of embodiments         1-78, wherein the RT domain comprises an amino acid sequence of         an FLV RT domain (e.g., as described in Table 6), or a sequence         having at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or         100% identity thereto.     -   83. The gene modifying polypeptide of any one of embodiments         1-78, wherein the RT domain comprises an amino acid sequence of         an FOAMV RT domain (e.g., as described in Table 6), or a         sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%,         99%, or 100% identity thereto.     -   84. The gene modifying polypeptide of any one of embodiments         1-78, wherein the RT domain comprises an amino acid sequence of         an GALV RT domain (e.g., as described in Table 6), or a sequence         having at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or         100% identity thereto.     -   85. The gene modifying polypeptide of any one of embodiments         1-78, wherein the RT domain comprises an amino acid sequence of         an KORV RT domain (e.g., as described in Table 6), or a sequence         having at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or         100% identity thereto.     -   86. The gene modifying polypeptide of any one of embodiments         1-78, wherein the RT domain comprises an amino acid sequence of         an MLVAV RT domain (e.g., as described in Table 6), or a         sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%,         99%, or 100% identity thereto.     -   87. The gene modifying polypeptide of any one of embodiments         1-78, wherein the RT domain comprises an amino acid sequence of         an MLVBM RT domain (e.g., as described in Table 6), or a         sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%,         99%, or 100% identity thereto.     -   88. The gene modifying polypeptide of any one of embodiments         1-78, wherein the RT domain comprises an amino acid sequence of         an MLVCB RT domain (e.g., as described in Table 6), or a         sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%,         99%, or 100% identity thereto.     -   89. The gene modifying polypeptide of any one of embodiments         1-78, wherein the RT domain comprises an amino acid sequence of         an MLVFF RT domain (e.g., as described in Table 6), or a         sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%,         99%, or 100% identity thereto.     -   90. The gene modifying polypeptide of any one of embodiments         1-78, wherein the RT domain comprises an amino acid sequence of         an MLVMS RT domain (e.g., as described in Table 6), or a         sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%,         99%, or 100% identity thereto.     -   91. The gene modifying polypeptide of any one of embodiments         1-78, wherein the RT domain comprises an amino acid sequence of         an PERV RT domain (e.g., as described in Table 6), or a sequence         having at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or         100% identity thereto.     -   92. The gene modifying polypeptide of any one of embodiments         1-78, wherein the RT domain comprises an amino acid sequence of         an SFV1 RT domain (e.g., as described in Table 6), or a sequence         having at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or         100% identity thereto.     -   93. The gene modifying polypeptide of any one of embodiments         1-78, wherein the RT domain comprises an amino acid sequence of         an SFV3L RT domain (e.g., as described in Table 6), or a         sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%,         99%, or 100% identity thereto.     -   94. The gene modifying polypeptide of any one of embodiments         1-78, wherein the RT domain comprises an amino acid sequence of         an WMSV RT domain (e.g., as described in Table 6), or a sequence         having at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or         100% identity thereto.     -   95. The gene modifying polypeptide of any one of embodiments         1-78, wherein the RT domain comprises an amino acid sequence of         an XMRV6 RT domain (e.g., as described in Table 6), or a         sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%,         99%, or 100% identity thereto.     -   96. The gene modifying polypeptide of any one of embodiments         1-78, wherein the RT domain comprises an amino acid sequence of         an MLVAV, MLVBM, BAEVM, FLV, FOAMV, GALV, KORV, AVIRE, MLVCB,         MLVFF, MLVMS, SFV3L, WMSV, or XMRV6 RT domain (e.g., as         described in Table 6), or a sequence having at least 70%, 75%,         80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% identity thereto.     -   97. The gene modifying polypeptide of any one of embodiments         1-78, wherein the RT domain comprises an amino acid sequence of         a gammaretroviral RT domain, or a sequence having at least 70%,         75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% identity         thereto.     -   98. The gene modifying polypeptide of embodiment 97, wherein the         RT domain comprises an amino acid sequence of an GALV, MLVAV,         MLVBM, BAEVM, FLV, AVIRE, KORV, MLVCB, MLVFF, WMSV, XMRV6,         MLVMS, and PERV RT domain (e.g., as described in Table 6), or a         sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%,         99%, or 100% identity thereto.     -   99. The gene modifying polypeptide of any embodiment 40, wherein         the RT domain comprises an amino acid sequence of an RT domain         as listed in any one of Tables 1, A1, A5, D1-D12, T1, or T2, or         a sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 97%,         98%, or 99% identity thereto.     -   100. The gene modifying polypeptide of embodiment 40, wherein         the linker comprises an amino acid sequence of a linker as         listed in any one of Tables 1, A1, A5, D1-D12, T1, or T2, or a         sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%,         or 99% identity thereto.     -   101. The gene modifying polypeptide of embodiment 40,         -   wherein the RT domain comprises an amino acid sequence of an             RT domain as listed in any one of Tables 1, A1, A5, D1-D12,             T1, or T2, or a sequence having at least 70%, 75%, 80%, 85%,             90%, 95%, 97%, 98%, or 99% identity thereto; and         -   wherein the linker comprises an amino acid sequence of a             linker as listed the same row of Table 1, A1, A5, D1-D12,             T1, or T2, or a sequence having at least 70%, 75%, 80%, 85%,             90%, 95%, 97%, 98%, or 99% identity thereto.     -   102. The gene modifying polypeptide of embodiment 40, wherein         the RT domain comprises one or more (e.g., at least 1, 2, 3, 4,         5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20)         amino acid substitutions at a residue corresponding to position         200, 603, 330, 524, 562, 583, 51, 67, 67, 197, 204, 302, 309,         313, 435, 454, 594, 671, 69, or 653 of an MLVMS RT domain         sequence as described herein (e.g., as listed in Table 6), e.g.,         an MLVMS_reference sequence, e.g., SEQ ID NO: 8137, relative to         a wildtype sequence of the RT domain.     -   103. The gene modifying polypeptide of embodiment 40, wherein         the RT domain comprises an RT domain comprising an amino acid         sequence of an MLVMS RT domain sequence as described herein         (e.g., as listed in Table 6), e.g., an MLVMS_reference sequence,         e.g., SEQ ID NO: 8137, or a sequence having at least 70%, 75%,         80%, 85%, 90%, 95%, 97%, 98%, or 99% identity thereto.     -   104. The gene modifying polypeptide of embodiment 40, wherein         the RT domain comprises one or more (e.g., at least 1, 2, 3, 4,         5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20)         amino acid substitutions at a residue corresponding to position         200, 603, 330, 524, 562, 583, 51, 67, 67, 197, 204, 302, 309,         313, 435, 454, 594, 671, 69, or 653 of an MLVMS RT domain         sequence as described herein (e.g., as listed in Table 6), e.g.,         an MLVMS_P03355 sequence, e.g., SEQ ID NO: 8070, relative to a         wildtype sequence of the RT domain.     -   105. The gene modifying polypeptide of embodiment 40, wherein         the RT domain comprises an RT domain comprising an amino acid         sequence of an MLVMS RT domain sequence as described herein         (e.g., as listed in Table 6), e.g., an MLVMS_P03355 sequence,         e.g., SEQ ID NO: 8070, or a sequence having at least 70%, 75%,         80%, 85%, 90%, 95%, 97%, 98%, or 99% identity thereto.     -   106. The gene modifying polypeptide of embodiment 40, wherein         the RT domain comprises an RT domain comprising an amino acid         sequence of an AVIRE RT domain sequence as described herein         (e.g., as listed in Table 6), e.g., an AVIRE_P03360 sequence,         e.g., SEQ ID NO: 8001, or a sequence having at least 70%, 75%,         80%, 85%, 90%, 95%, 97%, 98%, or 99% identity thereto.     -   107. The gene modifying polypeptide of embodiment 40, wherein         the RT domain comprises an RT domain comprising an amino acid         sequence of an BAEVM RT domain sequence as described herein         (e.g., as listed in Table 6), e.g., an BAEVM_P10272 sequence,         e.g., SEQ ID NO: 8004, or a sequence having at least 70%, 75%,         80%, 85%, 90%, 95%, 97%, 98%, or 99% identity thereto.     -   108. The gene modifying polypeptide of embodiment 40, wherein         the RT domain comprises an RT domain comprising an amino acid         sequence of an BLVAU RT domain sequence as described herein         (e.g., as listed in Table 6), e.g., an BLVAU_P25059 sequence,         e.g., SEQ ID NO: 8007, or a sequence having at least 70%, 75%,         80%, 85%, 90%, 95%, 97%, 98%, or 99% identity thereto.     -   109. The gene modifying polypeptide of embodiment 40, wherein         the RT domain comprises an RT domain comprising an amino acid         sequence of an BLVJ RT domain sequence as described herein         (e.g., as listed in Table 6), e.g., an BLVJ_P03361 sequence,         e.g., SEQ ID NO: 8009, or a sequence having at least 70%, 75%,         80%, 85%, 90%, 95%, 97%, 98%, or 99% identity thereto.     -   110. The gene modifying polypeptide of embodiment 40, wherein         the RT domain comprises an RT domain comprising an amino acid         sequence of an FFV RT domain sequence as described herein (e.g.,         as listed in Table 6), e.g., an FFV_O93209 sequence, e.g., SEQ         ID NO: 8012, or a sequence having at least 70%, 75%, 80%, 85%,         90%, 95%, 97%, 98%, or 99% identity thereto.     -   111. The gene modifying polypeptide of embodiment 40, wherein         the RT domain comprises an RT domain comprising an amino acid         sequence of an FLV RT domain sequence as described herein (e.g.,         as listed in Table 6), e.g., an FLV_P10273 sequence, e.g., SEQ         ID NO: 8019, or a sequence having at least 70%, 75%, 80%, 85%,         90%, 95%, 97%, 98%, or 99% identity thereto.     -   112. The gene modifying polypeptide of embodiment 40, wherein         the RT domain comprises an RT domain comprising an amino acid         sequence of an FOAMV RT domain sequence as described herein         (e.g., as listed in Table 6), e.g., an FOAMV_P14350 sequence,         e.g., SEQ ID NO: 8021, or a sequence having at least 70%, 75%,         80%, 85%, 90%, 95%, 97%, 98%, or 99% identity thereto.     -   113. The gene modifying polypeptide of embodiment 40, wherein         the RT domain comprises an RT domain comprising an amino acid         sequence of an GALV RT domain sequence as described herein         (e.g., as listed in Table 6), e.g., an GALV_P21414 sequence,         e.g., SEQ ID NO: 8027, or a sequence having at least 70%, 75%,         80%, 85%, 90%, 95%, 97%, 98%, or 99% identity thereto.     -   114. The gene modifying polypeptide of embodiment 40, wherein         the RT domain comprises an RT domain comprising an amino acid         sequence of an HTL1A RT domain sequence as described herein         (e.g., as listed in Table 6), e.g., an HTL1A_P03362 sequence,         e.g., SEQ ID NO: 8030, or a sequence having at least 70%, 75%,         80%, 85%, 90%, 95%, 97%, 98%, or 99% identity thereto.     -   115. The gene modifying polypeptide of embodiment 40, wherein         the RT domain comprises an RT domain comprising an amino acid         sequence of an HTL1C RT domain sequence as described herein         (e.g., as listed in Table 6), e.g., an HTL1C_P14078 sequence,         e.g., SEQ ID NO: 8033, or a sequence having at least 70%, 75%,         80%, 85%, 90%, 95%, 97%, 98%, or 99% identity thereto.     -   116. The gene modifying polypeptide of embodiment 40, wherein         the RT domain comprises an RT domain comprising an amino acid         sequence of an HTL32 RT domain sequence as described herein         (e.g., as listed in Table 6), e.g., an HTL32_Q0R5R2 sequence,         e.g., SEQ ID NO: 8038, or a sequence having at least 70%, 75%,         80%, 85%, 90%, 95%, 97%, 98%, or 99% identity thereto.     -   117. The gene modifying polypeptide of embodiment 40, wherein         the RT domain comprises an RT domain comprising an amino acid         sequence of an HTL3P RT domain sequence as described herein         (e.g., as listed in Table 6), e.g., an HTL3P_Q4U0X6 sequence,         e.g., SEQ ID NO: 8041, or a sequence having at least 70%, 75%,         80%, 85%, 90%, 95%, 97%, 98%, or 99% identity thereto.     -   118. The gene modifying polypeptide of embodiment 40, wherein         the RT domain comprises an RT domain comprising an amino acid         sequence of an JSRV RT domain sequence as described herein         (e.g., as listed in Table 6), e.g., an JSRV_P31623 sequence,         e.g., SEQ ID NO: 8045, or a sequence having at least 70%, 75%,         80%, 85%, 90%, 95%, 97%, 98%, or 99% identity thereto.     -   119. The gene modifying polypeptide of embodiment 40, wherein         the RT domain comprises an RT domain comprising an amino acid         sequence of an KORV RT domain sequence as described herein         (e.g., as listed in Table 6), e.g., an KORV_Q9TTC1 sequence,         e.g., SEQ ID NO: 8047, or a sequence having at least 70%, 75%,         80%, 85%, 90%, 95%, 97%, 98%, or 99% identity thereto.     -   120. The gene modifying polypeptide of embodiment 40, wherein         the RT domain comprises an RT domain comprising an amino acid         sequence of an MLVAV RT domain sequence as described herein         (e.g., as listed in Table 6), e.g., an MLVAV_P03356 sequence,         e.g., SEQ ID NO: 8053, or a sequence having at least 70%, 75%,         80%, 85%, 90%, 95%, 97%, 98%, or 99% identity thereto.     -   121. The gene modifying polypeptide of embodiment 40, wherein         the RT domain comprises an RT domain comprising an amino acid         sequence of an MLVBM RT domain sequence as described herein         (e.g., as listed in Table 6), e.g., an MLVBM_Q7SVK7 sequence,         e.g., SEQ ID NO: 8056, or a sequence having at least 70%, 75%,         80%, 85%, 90%, 95%, 97%, 98%, or 99% identity thereto.     -   122. The gene modifying polypeptide of embodiment 40, wherein         the RT domain comprises an RT domain comprising an amino acid         sequence of an MLVCB RT domain sequence as described herein         (e.g., as listed in Table 6), e.g., an MLVCB_P08361 sequence,         e.g., SEQ ID NO: 8062, or a sequence having at least 70%, 75%,         80%, 85%, 90%, 95%, 97%, 98%, or 99% identity thereto.     -   123. The gene modifying polypeptide of embodiment 40, wherein         the RT domain comprises an RT domain comprising an amino acid         sequence of an MLVF5 RT domain sequence as described herein         (e.g., as listed in Table 6), e.g., an MLVF5_P26810 sequence,         e.g., SEQ ID NO: 8065, or a sequence having at least 70%, 75%,         80%, 85%, 90%, 95%, 97%, 98%, or 99% identity thereto.     -   124. The gene modifying polypeptide of embodiment 40, wherein         the RT domain comprises an RT domain comprising an amino acid         sequence of an MLVRD RT domain sequence as described herein         (e.g., as listed in Table 6), e.g., an MLVRD_P11227 sequence,         e.g., SEQ ID NO: 8078, or a sequence having at least 70%, 75%,         80%, 85%, 90%, 95%, 97%, 98%, or 99% identity thereto.     -   125. The gene modifying polypeptide of embodiment 40, wherein         the RT domain comprises an RT domain comprising an amino acid         sequence of an MMTVB RT domain sequence as described herein         (e.g., as listed in Table 6), e.g., an MMTVB_P03365 sequence,         e.g., SEQ ID NO: 8080, or a sequence having at least 70%, 75%,         80%, 85%, 90%, 95%, 97%, 98%, or 99% identity thereto.     -   126. The gene modifying polypeptide of embodiment 40, wherein         the RT domain comprises an RT domain comprising an amino acid         sequence of an MPMV RT domain sequence as described herein         (e.g., as listed in Table 6), e.g., an MPMV_P07572 sequence,         e.g., SEQ ID NO: 8097, or a sequence having at least 70%, 75%,         80%, 85%, 90%, 95%, 97%, 98%, or 99% identity thereto.     -   127. The gene modifying polypeptide of embodiment 40, wherein         the RT domain comprises an RT domain comprising an amino acid         sequence of an PERV RT domain sequence as described herein         (e.g., as listed in Table 6), e.g., an PERV_Q4VFZ2 sequence,         e.g., SEQ ID NO: 8099, or a sequence having at least 70%, 75%,         80%, 85%, 90%, 95%, 97%, 98%, or 99% identity thereto.     -   128. The gene modifying polypeptide of embodiment 40, wherein         the RT domain comprises an RT domain comprising an amino acid         sequence of an SFV1 RT domain sequence as described herein         (e.g., as listed in Table 6), e.g., an SFV1_P23074 sequence,         e.g., SEQ ID NO: 8105, or a sequence having at least 70%, 75%,         80%, 85%, 90%, 95%, 97%, 98%, or 99% identity thereto.     -   129. The gene modifying polypeptide of embodiment 40, wherein         the RT domain comprises an RT domain comprising an amino acid         sequence of an SFV3L RT domain sequence as described herein         (e.g., as listed in Table 6), e.g., an SFV3L_P27401 sequence,         e.g., SEQ ID NO: 8111, or a sequence having at least 70%, 75%,         80%, 85%, 90%, 95%, 97%, 98%, or 99% identity thereto.     -   130. The gene modifying polypeptide of embodiment 40, wherein         the RT domain comprises an RT domain comprising an amino acid         sequence of an SFVCP RT domain sequence as described herein         (e.g., as listed in Table 6), e.g., an SFVCP_Q87040 sequence,         e.g., SEQ ID NO: 8117, or a sequence having at least 70%, 75%,         80%, 85%, 90%, 95%, 97%, 98%, or 99% identity thereto.     -   131. The gene modifying polypeptide of embodiment 40, wherein         the RT domain comprises an RT domain comprising an amino acid         sequence of an SMRV RT domain sequence as described herein         (e.g., as listed in Table 6), e.g., an SMRVH_P03364 sequence,         e.g., SEQ ID NO: 8123, or a sequence having at least 70%, 75%,         80%, 85%, 90%, 95%, 97%, 98%, or 99% identity thereto.     -   132. The gene modifying polypeptide of embodiment 40, wherein         the RT domain comprises an RT domain comprising an amino acid         sequence of an SRV2 RT domain sequence as described herein         (e.g., as listed in Table 6), e.g., an SRV2_P51517 sequence,         e.g., SEQ ID NO: 8126, or a sequence having at least 70%, 75%,         80%, 85%, 90%, 95%, 97%, 98%, or 99% identity thereto.     -   133. The gene modifying polypeptide of embodiment 40, wherein         the RT domain comprises an RT domain comprising an amino acid         sequence of an WDSV RT domain sequence as described herein         (e.g., as listed in Table 6), e.g., an WDSV_092815 sequence,         e.g., SEQ ID NO: 8128, or a sequence having at least 70%, 75%,         80%, 85%, 90%, 95%, 97%, 98%, or 99% identity thereto.     -   134. The gene modifying polypeptide of embodiment 40, wherein         the RT domain comprises an RT domain comprising an amino acid         sequence of an WMSV RT domain sequence as described herein         (e.g., as listed in Table 6), e.g., an WMSV_P03359 sequence,         e.g., SEQ ID NO: 8131, or a sequence having at least 70%, 75%,         80%, 85%, 90%, 95%, 97%, 98%, or 99% identity thereto.     -   135. The gene modifying polypeptide of embodiment 40, wherein         the RT domain comprises an RT domain comprising an amino acid         sequence of an XMRV6 RT domain sequence as described herein         (e.g., as listed in Table 6), e.g., an XMRV6_A1Z651 sequence,         e.g., SEQ ID NO: 8134, or a sequence having at least 70%, 75%,         80%, 85%, 90%, 95%, 97%, 98%, or 99% identity thereto.     -   136. The gene modifying polypeptide of any one of embodiments         40-135, wherein the RT domain comprises:         -   a) the amino acid asparagine (N) at position 200 of SEQ ID             NO: 8137 or at a corresponding position in a homologous RT             domain;         -   b) the amino acid tryptophan (W) at position 603 of SEQ ID             NO: 8137 or at a corresponding position in a homologous RT             domain;         -   c) the amino acid proline (P) at position 330 of SEQ ID NO:             8137 or at a corresponding position in a homologous RT             domain;         -   d) the amino acid glycine (G) at position 524 of SEQ ID NO:             8137 or at a corresponding position in a homologous RT             domain;         -   e) the amino acid glutamine (Q) at position 562 of SEQ ID             NO: 8137 or at a corresponding position in a homologous RT             domain;         -   f) the amino acid asparagine (N) at position 583 of SEQ ID             NO: 8137 or at a corresponding position in a homologous RT             domain;         -   g) the amino acid leucine (L) at position 51 of SEQ ID NO:             8137 or at a corresponding position in a homologous RT             domain;         -   h) the amino acid arginine (R) at position 67 of SEQ ID NO:             8137 or at a corresponding position in a homologous RT             domain;         -   i) the amino acid lysine (K) at position 67 of SEQ ID NO:             8137 or at a corresponding position in a homologous RT             domain;         -   j) the amino acid alanine (A) at position 197 of SEQ ID NO:             8137 or at a corresponding position in a homologous RT             domain;         -   k) the amino acid arginine (R) at position 204 of SEQ ID NO:             8137 or at a corresponding position in a homologous RT             domain;         -   l) the amino acid lysine (K) at position 302 of SEQ ID NO:             8137 or at a corresponding position in a homologous RT             domain;         -   m) the amino acid asparagine (N) at position 309 of SEQ ID             NO: 8137 or at a corresponding position in a homologous RT             domain;         -   n) the amino acid phenylalanine (F) at position 313 of SEQ             ID NO: 8137 or at a corresponding position in a homologous             RT domain;         -   o) the amino acid glycine (G) at position 435 of SEQ ID NO:             8137 or at a corresponding position in a homologous RT             domain;         -   p) the amino acid lysine (K) at position 454 of SEQ ID NO:             8137 or at a corresponding position in a homologous RT             domain;         -   q) the amino acid glutamine (Q) at position 594 of SEQ ID             NO: 8137 or at a corresponding position in a homologous RT             domain;         -   r) the amino acid proline (P) at position 671 of SEQ ID NO:             8137 or at a corresponding position in a homologous RT             domain;         -   s) the amino acid lysine (K) at position 69 of SEQ ID NO:             8137 or at a corresponding position in a homologous RT             domain; or         -   t) the amino acid asparagine (N) at position 653 of SEQ ID             NO: 8137 or at a corresponding position in a homologous RT             domain.     -   137. The gene modifying polypeptide of embodiment 40, wherein         the RT domain has a sequence with at least 90% identity to the         RT domain of the reference gene modifying polypeptide.     -   138. The gene modifying polypeptide of any of the preceding         embodiments, wherein the RT domain has a sequence with at least         95% identity to the RT domain of the reference gene modifying         polypeptide.     -   139. The gene modifying polypeptide of any of the preceding         embodiments, wherein the RT domain has a sequence with at least         98% identity to the RT domain of the reference gene modifying         polypeptide.     -   140. The gene modifying polypeptide of any of the preceding         embodiments, wherein the RT domain has a sequence with at least         99% identity to the RT domain of the reference gene modifying         polypeptide.     -   141. The gene modifying polypeptide of any of the preceding         embodiments, wherein the RT domain has a sequence with 100%         identity to the RT domain of the reference gene modifying         polypeptide.     -   142. The gene modifying polypeptide of any of the preceding         embodiments, wherein the linker has a sequence with at least 90%         identity to the linker sequence from the reference gene         modifying polypeptide.     -   143. The gene modifying polypeptide of any of the preceding         embodiments, wherein the linker has a sequence with at least 95%         identity to the linker sequence from the reference gene         modifying polypeptide.     -   144. The gene modifying polypeptide of any of the preceding         embodiments, wherein the linker has a sequence with at least 97%         identity to the linker sequence from the reference gene         modifying polypeptide.     -   145. The gene modifying polypeptide of any of the preceding         embodiments, wherein the linker has a sequence with 100%         identity to the linker sequence from the reference gene         modifying polypeptide.     -   146. The gene modifying polypeptide of any of the preceding         embodiments, wherein the linker has an amino acid sequence with         at least 80%, 85%, 90%, 95%, 97%, or 100% identity to SEQ ID NO:         11,041.     -   147. The gene modifying polypeptide of any of the preceding         embodiments, wherein the RT domain comprises a mutation as         listed in Table 2.     -   148. The gene modifying polypeptide of any of the preceding         embodiments, wherein the RT domain comprises one or more (e.g.,         1, 2, 3, 4, 5, or 6) mutations as listed in any single row of         Table 2.     -   149. The gene modifying polypeptide of any of the preceding         embodiments, wherein the RT domain comprises all of the         mutations listed in any single row of Table 2.     -   150. The gene modifying polypeptide of any of the preceding         embodiments, wherein the Cas domain comprises a sequence of         Table 7 or 8, or a sequence having at least 70%, 75%, 80%, 85%,         90%, 95%, 98%, or 99% identity thereto.     -   151. The gene modifying polypeptide of any of the preceding         embodiments, wherein the Cas domain comprises the amino acid         sequence of a Cas domain comprised in the amino acid sequence of         the reference gene modifying polypeptide, or a sequence having         at least 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 99% identity         thereto.     -   152. The gene modifying polypeptide of any of the preceding         embodiments, wherein the Cas domain does not comprise the amino         acid sequence of a Cas domain comprised in the amino acid         sequence of the reference gene modifying polypeptide, or a         sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 98%, or         99% identity thereto.     -   153. The gene modifying polypeptide of any of the preceding         embodiments, wherein the Cas domain is a Cas nickase domain.     -   154. The gene modifying polypeptide of any of the preceding         embodiments, wherein the Cas domain is a Cas9 nickase domain.     -   155. The gene modifying polypeptide of any of the preceding         embodiments, wherein the Cas domain comprises an N863A mutation.     -   156. The gene modifying polypeptide of any of the preceding         embodiments, which comprises an NLS, e.g., wherein the gene         modifying polypeptide comprises two NLSs.     -   157. The gene modifying polypeptide of any of the preceding         embodiments, which comprises an NLS N-terminal of the Cas9         domain.     -   158. The gene modifying polypeptide of any of the preceding         embodiments, which comprises an NLS C-terminal of the RT domain.     -   159. The gene modifying polypeptide of any of the preceding         embodiments, which comprises a first NLS which is N-terminal of         the Cas9 domain and a second NLS which is C-terminal of the RT         domain.     -   160. The gene modifying polypeptide of any of the preceding         embodiments, which comprises a sequence of SEQ ID NO: 4000 which         comprises the first NLS and the Cas domain, or a sequence having         at least 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 99% identity         thereto.     -   161. The gene modifying polypeptide of any of the preceding         embodiments, which comprises a sequence of SEQ ID NO: 4001 which         comprises the second NLS, or a sequence having at least 70%,         75%, 80%, 85%, 90%, 95%, 98%, or 99% identity thereto.     -   162. The gene modifying polypeptide of any of the preceding         embodiments, which comprises a GG amino acid sequence between         the Cas domain and the linker.     -   163. The gene modifying polypeptide of any of the preceding         embodiments, which comprises an AG amino acid sequence between         the RT domain and the second NLS.     -   164. The gene modifying polypeptide of any of the preceding         embodiments, which comprises a GG amino acid sequence between         the linker and the RT domain.     -   165. The gene modifying polypeptide of any of the preceding         embodiments, which produces an increase in converted GFP+ of at         least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 75%, 80%, 85%, 90%,         95%, 100%, 125%, 150%, 175%, 200%, 250%, 300%, 400%, 500%, 600%,         700%, 800%, 900%, 1000%, 1500%, 2000%, or 2500% relative to         unsorted input cells in an assay of Example 2 using HEK cells         and g4 guide RNA.     -   166. A gene modifying polypeptide comprising:         -   a Cas domain (e.g., a Cas nickase domain, e.g., a Cas9             nickase domain);         -   a reverse transcriptase (RT) domain comprising an amino acid             sequence of an RT domain provided in any one of SEQ ID NOs:             1-7743, or a sequence having at least 70%, 75%, 80%, 85%,             90%, 95%, 97%, 98%, or 99% identity thereto; and         -   a linker disposed between the RT domain and the Cas domain             comprising an amino acid sequence of a linker as listed in             Table 10, or a sequence having at least 70%, 75%, 80%, 85%,             90%, 95%, 97%, 98%, or 99% identity thereto,         -   wherein the amino acid sequences of the RT domain and the             linker are provided in the same amino acid sequence of any             one of SEQ ID NOs: 1-7743,         -   which produces an increase in converted GFP+ of at least             10%, 20%, 30%, 40%, 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95%,             100%, 125%, 150%, 175%, 200%, 250%, 300%, 400%, 500%, 600%,             700%, 800%, 900%, 1000%, 1500%, 2000%, or 2500% relative to             unsorted input cells in an assay of Example 2 using HEK             cells and g4 guide RNA.     -   167. The gene modifying polypeptide of any of the preceding         embodiments, which has an activity that is at least 50%, 60%,         70%, 80%, or 90% of the activity of a reference gene modifying         polypeptide comprising, in an N-terminal to C-terminal         direction:         -   a) an NLS and Cas domain sequence of SEQ ID NO: 4000;         -   b) a linker having the sequence EAAAKGSS (SEQ ID NO: 5152);         -   c) an RT domain having the sequence of PERV_Q4VFZ2_3mutA_WS;             and         -   d) an NLS sequence of SEQ ID NO: 4001, in an assay of             Example 1 using HEK cells and g4 guide RNA.     -   168. The gene modifying polypeptide of any of the preceding         embodiments, which has an activity that is at least 10%, 20%,         30%, 40%, 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 125%,         150%, 175%, 200%, 250%, 300%, 400%, 500%, 600%, 700%, 800%,         900%, 1000%, 1500%, 2000%, or 2500% greater than the activity of         a reference gene modifying polypeptide comprising a sequence of         SEQ ID NO: 4002, e.g., in an assay of Example 1 using HEK cells         and g4 guide RNA.     -   169. A nucleic acid (e.g., DNA or RNA, e.g., mRNA) encoding the         gene modifying polypeptide of any of the preceding embodiments.     -   170. A cell comprising the gene modifying polypeptide of any of         embodiments 40-68 or the nucleic acid of embodiment 169.     -   171. A system comprising:         -   i) the gene modifying polypeptide of any of embodiments             40-68, and         -   ii) a template RNA that comprises:             -   a) a gRNA spacer that is complementary to a portion a                 target nucleic acid sequence;             -   b) a gRNA scaffold that binds the Cas domain of the gene                 modifying polypeptide;             -   c) a heterologous object sequence; and             -   d) a primer binding site sequence (PBS sequence).     -   172. A method for modifying a target nucleic acid in a cell         (e.g., a human cell), the method comprising contacting the cell         with the system of embodiment 171, or nucleic acid encoding the         same, thereby modifying the target nucleic acid.     -   173. A gene modifying polypeptide comprising:         -   a Cas domain (e.g., a Cas nickase domain, e.g., a Cas9             nickase domain);         -   a reverse transcriptase (RT) domain having one or more             (e.g., at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,             14, 15, 16, 17, 18, 19, or 20) amino acid substitutions at a             residue corresponding to (e.g., at a residue at a homologous             position relative to) position 200, 603, 330, 524, 562, 583,             51, 67, 67, 197, 204, 302, 309, 313, 435, 454, 594, 671, 69,             or 653 of an MLVMS RT domain sequence as described herein             (e.g., as listed in Table 6), e.g., an MLVMS_reference             sequence, e.g., SEQ ID NO: 8137 relative to a wildtype             sequence of the RT domain, wherein the RT domain is             C-terminal of the Cas domain; and         -   a linker disposed between the RT domain and the Cas domain,             wherein the linker has a sequence from the same row of Table             1 as the RT domain, or a sequence having at least 70%, 75%,             80%, 85%, 90%, 95%, 97%, 98%, or 99% identity thereto.     -   174. A gene modifying polypeptide comprising:         -   a reverse transcriptase (RT) domain of an AVIRE RT, or an             amino acid sequence having at least 70%, 75%, 80%, 85%, 90%,             95%, 96%, 97%, 98%, or 99% identity thereto;         -   a Cas nickase domain, wherein the RT domain is C-terminal of             the Cas domain; and         -   a linker disposed between the Cas nickase domain and the RT             domain, wherein the linker comprises an amino acid sequence             as listed in Table 10, or an amino acid sequence having at             least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99%             identity thereto.     -   175. A gene modifying polypeptide comprising:         -   a reverse transcriptase (RT) domain comprising the RT domain             of a reference gene modifying polypeptide having sequence of             any one of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 9, 10, 12, 13,             14, 6076, 6143, 6200, 6254, 6274, 6315, 6328, 6337, 6403,             6420, 6440, 6513, 6552, 6613, 6671, 6822, 6840, 6884, 6907,             6970, 7025, 7052, 7078, 7243, 7253, 7318, 7379, 7486, 7524,             7668, 7680, 7720, 1137, 1138, 1139, 1140, 1141, 1142, 1143,             1144, 1145, 1146, 1147, 1148, 1149, 1150, 1151, 1152, 1153,             1154, 1155, 1156, 1157, 1158, 1159, 1160, 1161, 1162, 1163,             1164, 1165, 1166, 1167, 6015, 6029, 6045, 6077, 6129, 6144,             6164, 6201, 6227, 6244, 6250, 6264, 6289, 6304, 6316, 6384,             6421, 6441, 6492, 6514, 6530, 6569, 6584, 6621, 6651, 6659,             6683, 6703, 6727, 6732, 6745, 6755, 6784, 6817, 6823, 6841,             6871, 6885, 6898, 6908, 6933, 6971, 7009, 7018, 7045, 7053,             7068, 7079, 7096, 7104, 7122, 7151, 7163, 7181, 7244, 7273,             7319, 7336, 7380, 7402, 7462, 7487, 7525, 7569, 7626, 7689,             7707, 7721, 1371, 1372, 1373, 1374, 1375, 1376, 1377, 1378,             1379, 1380, 1381, 1382, 1383, 1384, 1385, 1386, 1387, 1388,             1389, 1390, 1391, 1392, 1393, 1394, 1395, 1396, 1397, 1398,             1399, 1400, 1401, 1402, 1403, 1404, 1405, 1406, 1407, 1408,             1409, 1410, 1411, 1412, 1413, 1414, 1415, 1416, 1417, 1418,             1419, 1420, 1421, 1422, 1423, 1424, 1425, 1426, 1427, 1428,             1429, 1430, 1431, 1432, 1433, 1434, 1435, 1436, 1437, 1439,             1440, 1441, 1442, 1443, 1444, 1445, 1446, 1447, 6001, 6030,             6078, 6108, 6130, 6165, 6265, 6275, 6305, 6329, 6370, 6385,             6404, 6531, 6585, 6622, 6652, 6733, 6756, 6765, 6798, 6824,             6972, 7046, 7054, 7069, 7080, 7105, 7123, 7143, 7152, 7204,             7320, 7351, 7381, 7403, 7438, 7488, 7500, 7526, 7588, 7612,             7627 or a sequence having at least 70%, 75%, 80%, 85%, 90%,             95%, 97%, 98%, or 99% identity thereto;         -   a Cas nickase domain, wherein the RT domain is C-terminal of             the Cas domain; and         -   a linker disposed between the Cas nickase domain and the RT             domain, wherein the linker comprises the linker of said             reference gene modifying polypeptide, or a sequence having             at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%             identity thereto.     -   176. A gene modifying polypeptide comprising:         -   a reverse transcriptase (RT) domain having the sequence of             SEQ ID NO: 8001, 8002, or 8003, or a sequence having at             least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%             identity thereto;         -   a Cas nickase domain, wherein the RT domain is C-terminal of             the Cas nickase domain; and         -   a linker disposed between the RT domain and the Cas nickase             domain, wherein the linker comprises an amino acid sequence             of the linker of any of SEQ ID NOS: a reference gene             modifying polypeptide having sequence of any one of SEQ ID             NO: 1, 2, 3, 4, 5, 6, 7, 9, 10, 12, 13, 14, 6076, 6143,             6200, 6254, 6274, 6315, 6328, 6337, 6403, 6420, 6440, 6513,             6552, 6613, 6671, 6822, 6840, 6884, 6907, 6970, 7025, 7052,             7078, 7243, 7253, 7318, 7379, 7486, 7524, 7668, 7680, 7720,             1137, 1138, 1139, 1140, 1141, 1142, 1143, 1144, 1145, 1146,             1147, 1148, 1149, 1150, 1151, 1152, 1153, 1154, 1155, 1156,             1157, 1158, 1159, 1160, 1161, 1162, 1163, 1164, 1165, 1166,             1167, 6015, 6029, 6045, 6077, 6129, 6144, 6164, 6201, 6227,             6244, 6250, 6264, 6289, 6304, 6316, 6384, 6421, 6441, 6492,             6514, 6530, 6569, 6584, 6621, 6651, 6659, 6683, 6703, 6727,             6732, 6745, 6755, 6784, 6817, 6823, 6841, 6871, 6885, 6898,             6908, 6933, 6971, 7009, 7018, 7045, 7053, 7068, 7079, 7096,             7104, 7122, 7151, 7163, 7181, 7244, 7273, 7319, 7336, 7380,             7402, 7462, 7487, 7525, 7569, 7626, 7689, 7707, 7721, 1371,             1372, 1373, 1374, 1375, 1376, 1377, 1378, 1379, 1380, 1381,             1382, 1383, 1384, 1385, 1386, 1387, 1388, 1389, 1390, 1391,             1392, 1393, 1394, 1395, 1396, 1397, 1398, 1399, 1400, 1401,             1402, 1403, 1404, 1405, 1406, 1407, 1408, 1409, 1410, 1411,             1412, 1413, 1414, 1415, 1416, 1417, 1418, 1419, 1420, 1421,             1422, 1423, 1424, 1425, 1426, 1427, 1428, 1429, 1430, 1431,             1432, 1433, 1434, 1435, 1436, 1437, 1439, 1440, 1441, 1442,             1443, 1444, 1445, 1446, 1447, 6001, 6030, 6078, 6108, 6130,             6165, 6265, 6275, 6305, 6329, 6370, 6385, 6404, 6531, 6585,             6622, 6652, 6733, 6756, 6765, 6798, 6824, 6972, 7046, 7054,             7069, 7080, 7105, 7123, 7143, 7152, 7204, 7320, 7351, 7381,             7403, 7438, 7488, 7500, 7526, 7588, 7612, 7627, or a             sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 97%,             98%, or 99% identity thereto.     -   177. The gene modifying polypeptide of any of embodiments         174-176, wherein the RT domain comprises a mutation at one or         more of positions 8, 51, 67, 69, 197, 200, 204, 302, 306, 309,         313, 330, 436, 455, 526, 564, 585, 596, 605, 655, 673 relative         to a reference RT domain having sequence of SEQ ID NO:8001.     -   178. The gene modifying polypeptide of any of embodiments         174-177, wherein the RT domain comprises one or more of the         following mutations: Q51L, T67R, E67K, E69K, T197A, D200N,         N204R, E302K, Y309N, W313F, G330P, T436G, N455K, D526G, E564Q,         D585N, H596Q, L605W, D655N, L673P     -   179. The gene modifying polypeptide of embodiment 178, wherein         the RT domain comprises the following mutations: (a) D200N,         G330P, and L605W or (b) D200N, G330P, L605W, T306K, and W313F.     -   180. The gene modifying polypeptide of any of embodiments         174-179, said polypeptide comprising a linker having a sequence         of any one of SEQ ID NO: 11,041-11,050.     -   181. A gene modifying polypeptide comprising:         -   a reverse transcriptase (RT) domain having the sequence of             SEQ ID NO: 8,003, or a sequence having at least 95% identity             thereto;         -   a Cas nickase domain, wherein the RT domain is C-terminal of             the Cas nickase domain; and         -   a linker disposed between the RT domain and the Cas nickase             domain, wherein the linker comprises an amino acid sequence             according to SEQ ID NO: 5217 or 15,401.     -   182. A gene modifying polypeptide comprising:         -   a reverse transcriptase (RT) domain having the sequence of             SEQ ID NO: 8,020, or a sequence having at least 95% identity             thereto;         -   a Cas nickase domain, wherein the RT domain is C-terminal of             the Cas nickase domain; and         -   a linker disposed between the RT domain and the Cas nickase             domain, wherein the linker comprises an amino acid sequence             according to SEQ ID NO: 5217 or 15,402.     -   183. A gene modifying polypeptide comprising:         -   a reverse transcriptase (RT) domain having the sequence of             SEQ ID NO: 8,074, or a sequence having at least 95% identity             thereto;         -   a Cas nickase domain, wherein the RT domain is C-terminal of             the Cas nickase domain; and         -   a linker disposed between the RT domain and the Cas nickase             domain, wherein the linker comprises an amino acid sequence             according to SEQ ID NO: 15,403.     -   184. A gene modifying polypeptide comprising:         -   a reverse transcriptase (RT) domain having the sequence of             SEQ ID NO: 8,113, or a sequence having at least 95% identity             thereto;         -   a Cas nickase domain, wherein the RT domain is C-terminal of             the Cas nickase domain; and         -   a linker disposed between the RT domain and the Cas nickase             domain, wherein the linker comprises an amino acid sequence             according to SEQ ID NO: 15,404.     -   185. A gene modifying polypeptide comprising:         -   a reverse transcriptase (RT) domain comprising the RT domain             of a reference gene modifying polypeptide having the             sequence of any one of SEQ ID NOs: 1-7743; and         -   a Cas nickase domain, wherein the RT domain is C-terminal of             the Cas nickase domain; and         -   a linker disposed between the RT domain and the Cas nickase             domain, wherein the linker comprises the linker of said             reference gene modifying polypeptide.     -   186. The gene modifying polypeptide of any of embodiments         174-185, which comprises a nuclear localization signal (NLS).     -   187. The gene modifying polypeptide of any of embodiments         174-186, which comprises a first NLS which is N-terminal of the         Cas nickase domain.     -   188. The gene modifying polypeptide of any of embodiments         174-187, which comprises an NLS which is C-terminal of the RT         domain.     -   189. The gene modifying polypeptide of any of embodiments         174-188, which comprises a first NLS which is N-terminal of the         Cas nickase domain and a second NLS which is C-terminal of the         RT domain.     -   190. The gene modifying polypeptide of any of embodiments         174-189, which comprises a first NLS which is N-terminal of the         Cas nickase domain, wherein the first NLS comprises an amino         acid sequence of PAAKRVKLD (SEQ ID NO: 11,095).     -   191. The gene modifying polypeptide of any of embodiments         174-190, which comprises an NLS which is C-terminal of the RT         domain and has an amino acid sequence of KRTADGSEFE (SEQ ID NO:         4650).     -   192. The gene modifying polypeptide of any of embodiments         174-191, which comprises an NLS which is C-terminal of the RT         domain and has an amino acid sequence of KRTADGSEFESPKKKAKVE         (SEQ ID NO: 4651).     -   193. The gene modifying polypeptide of any of embodiments         174-192, which comprises a sequence of SEQ ID NO: 4000 which         comprises the first NLS and the Cas nickase domain.     -   194. The gene modifying polypeptide of any of embodiments         174-193, which comprises a sequence of SEQ ID NO: 4001 which         comprises the second NLS.     -   195. The gene modifying polypeptide of any of embodiments         174-194, which comprises a GG amino acid sequence between the         Cas nickase domain and the linker.     -   196. The gene modifying polypeptide of any of embodiments         174-195, which comprises an AG amino acid sequence between the         RT domain and the second NLS.     -   197. The gene modifying polypeptide of any of embodiments         174-196, which comprises a GG amino acid sequence between the         linker and the RT domain.     -   198. The gene modifying polypeptide of any of embodiments         174-197, wherein the Cas nickase domain comprises a Cas9 nickase         domain.     -   199. The gene modifying polypeptide of any of embodiments         174-198, wherein the Cas nickase domain comprises an N863A         mutation.     -   200. The gene modifying polypeptide of any of embodiments         174-199, wherein the Cas nickase comprises a sequence of SEQ ID         NO: 11,096.     -   201. The gene modifying polypeptide of any of embodiments         174-200, wherein the Cas nickase comprises a sequence of any of         SEQ ID NO: 9,001-9,037, 11,096, or a sequence having at least         70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% identity thereto.     -   202. The gene modifying polypeptide of any of embodiments         174-201, which comprises a methionine at the N-terminal position         of the RT domain.     -   203. The gene modifying polypeptide of any of embodiments         174-202, which does not comprises a methionine at the N-terminal         position of the RT domain.     -   204. The gene modifying polypeptide of any of embodiments         174-203, which comprises an amino acid sequence according to any         of SEQ ID NOs: 1372, 1373, or 1410 or an amino acid sequence         having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or         99% identity thereto.     -   205. The gene modifying polypeptide of any of embodiments         174-204, which comprises an amino acid sequence according to SEQ         ID NO: 2784 or an amino acid sequence having at least 70%, 75%,         80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto.     -   206. The gene modifying polypeptide of any of embodiments         174-205, which comprises an amino acid sequence according to SEQ         ID NO: 647 or an amino acid sequence having at least 70%, 75%,         80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto.     -   207. The gene modifying polypeptide of any of embodiments         174-206, which comprises an amino acid sequence according to SEQ         ID NO: 1197 or an amino acid sequence having at least 70%, 75%,         80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto.     -   208. A nucleic acid molecule encoding the gene modifying         polypeptide of any of embodiments 174-207.     -   209. The nucleic acid molecule of embodiment 208, which         comprises RNA.     -   210. The nucleic acid molecule of embodiment 209, which         comprises mRNA.     -   211. A cell comprising the gene modifying polypeptide of any of         embodiments 174-207.     -   212. A cell comprising the nucleic acid molecule of any of         embodiments 208-210.     -   213. A system comprising:         -   i) the gene modifying polypeptide of any of embodiments             174-207, or a nucleic acid molecule encoding the gene             modifying polypeptide, and         -   ii) a template RNA that comprises:             -   a) a gRNA spacer that is complementary to a portion a                 target nucleic acid sequence;             -   b) a gRNA scaffold that binds the Cas nickase domain of                 the gene modifying polypeptide;             -   c) a heterologous object sequence; and             -   d) a primer binding site sequence.     -   214. A lipid nanoparticle formulation comprising the gene         modifying polypeptide of any of embodiments 174-207, the nucleic         acid of any of embodiments 208-210, or the system of embodiment         213.     -   215. A method for modifying a target nucleic acid molecule in a         cell, the method comprising contacting the cell with the system         of embodiment 213, thereby modifying the target nucleic acid         molecule.     -   216. A method of using the gene modifying polypeptide of any of         embodiments 174-207, the nucleic acid of any of embodiments         208-210, or the system of embodiment 213, to modify a target         genome by target-primed reverse transcription, the method         comprising contacting the target genome with the gene modifying         polypeptide, nucleic acid, or system, thereby modifying the         target nucleic acid molecule.

In one aspect, the disclosure relates to a system for modifying DNA, comprising (a) a nucleic acid encoding a gene modifying polypeptide capable of target primed reverse transcription, the polypeptide comprising (i) a reverse transcriptase domain and (ii) a Cas9 nickase that binds DNA and has endonuclease activity, and (b) a template RNA comprising (i) a gRNA spacer that is complementary to a first portion of a human gene, (ii) a gRNA scaffold that binds the polypeptide, (iii) a heterologous object sequence comprising a mutation region, and (iv) a primer binding site (PBS) sequence comprising at least 3, 4, 5, 6, 7, or 8 bases of 100% homology to a target DNA strand at the 3′ end of the template RNA.

The gRNA spacer may comprise at least 15 bases of 100% homology to the target DNA at the 5′ end of the template RNA. The template RNA may further comprise a PBS sequence comprising at least 5 bases of at least 80% homology to the target DNA strand. The template RNA may comprise one or more chemical modifications.

The domains of the gene modifying polypeptide may be joined by a peptide linker. The polypeptide may comprise one or more peptide linkers. The gene modifying polypeptide may further comprise a nuclear localization signal. The polypeptide may comprise more than one nuclear localization signal, e.g., multiple adjacent nuclear localization signals or one or more nuclear localization signals in different regions of the polypeptide, e.g., one or more nuclear localization signals in the N-terminus of the polypeptide and one or more nuclear localization signals in the C-terminus of the polypeptide. The nucleic acid encoding the gene modifying polypeptide may encode one or more intein domains.

Introduction of the system into a target cell may result in insertion of at least 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 150, 200, 250, 300, 350, 400, 500, or 1000 base pairs of exogenous DNA. Introduction of the system into a target cell may result in deletion, wherein the deletion is less than 2, 3, 4, 5, 10, 50, or 100 base pairs of genomic DNA upstream or downstream of the insertion. Introduction of the system into a target cell may result in substitution, e.g., substitution of 1, 2, or 3 nucleotides, e.g., consecutive nucleotides.

The heterologous object sequence may be at least 5, 10, 25, 50, 100, 150, 200, 250, 300, 400, 500, 600, or 700 base pairs.

In one aspect, the disclosure relates to a pharmaceutical composition comprising the system described above and a pharmaceutically acceptable excipient or carrier, wherein the pharmaceutically acceptable excipient or carrier is selected from the group consisting of a plasmid vector, a viral vector, a vesicle, and a lipid nanoparticle. In one aspect, the disclosure relates to a pharmaceutical composition comprising the system described above and multiple pharmaceutically acceptable excipients or carriers, wherein the pharmaceutically acceptable excipients or carriers are selected from the group consisting of a plasmid vector, a viral vector, a vesicle, and a lipid nanoparticle, e.g., where the system described above is delivered by two distinct excipients or carriers, e.g., two lipid nanoparticles, two viral vectors, or one lipid nanoparticle and one viral vector. The viral vector may be an adeno-associated virus (AAV).

In one aspect, the disclosure relates to a host cell (e.g., a mammalian cell, e.g., a human cell) comprising the system described above.

The system may be introduced in vivo, in vitro, ex vivo, or in situ. The nucleic acid of (a) may be integrated into the genome of the host cell. In some embodiments, the nucleic acid of (a) is not integrated into the genome of the host cell. In some embodiments, the heterologous object sequence is inserted at only one target site in the host cell genome. The heterologous object sequence may be inserted at two or more target sites in the host cell genome, e.g., at the same corresponding site in two homologous chromosomes or at two different sites on the same or different chromosomes. The heterologous object sequence may encode a mammalian polypeptide, or a fragment or a variant thereof. The components of the system may be delivered on 1, 2, 3, 4, or more distinct nucleic acid molecules. The system may be introduced into a host cell by electroporation or by using at least one vehicle selected from a plasmid vector, a viral vector, a vesicle, and a lipid nanoparticle.

BRIEF DESCRIPTION OF THE DRAWINGS

The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.

FIG. 1 depicts a gene modifying system as described herein. The left hand diagram shows the gene modifying polypeptide, which comprises a Cas nickase domain (e.g., spCas9 N863A) and a reverse transcriptase domain (RT domain) which are linked by a linker. The right hand diagram shows the template RNA which comprises, from 5′ to 3′, a gRNA spacer, a gRNA scaffold, a heterologous object sequence, and a primer binding site sequence (PBS sequence). The heterologous object sequence can comprise a mutation region that comprises one or more sequence differences relative to the target site. The heterologous object sequence can also comprise a pre-edit homology region and a post-edit homology region, which flank the mutation region. Without wishing to be bound by theory, it is thought that the gRNA spacer of the template RNA binds to the second strand of a target site in the genome, and the gRNA scaffold of the template RNA binds to the gene modifying polypeptide, e.g., localizing the gene modifying polypeptide to the target site in the genome. It is thought that the Cas domain of the gene modifying polypeptide nicks the target site (e.g., the first strand of the target site), e.g., allowing the PBS sequence to bind to a sequence adjacent to the site to be altered on the first strand of the target site. It is thought that the RT domain of the gene modifying polypeptide uses the first strand of the target site that is bound to the complementary sequence comprising the PBS sequence of the template RNA as a primer and the heterologous object sequence of the template RNA as a template to, e.g., polymerize a sequence complementary to the heterologous object sequence. Without wishing to be bound by theory, it is thought that reverse transcription can then proceed through the pre-edit homology region, then through the mutation region, and then through the post-edit homology region, thereby producing a DNA strand comprising a mutation specified by the heterologous object sequence.

FIGS. 2A-2B provide schematics of a gene modifying polypeptide candidate for a screening library and a description of the screening methodology. FIG. 2A is a schematic of the gene modifying polypeptide candidate, a fusion polypeptide comprising a nuclear localization signal (NLS), a S. pyogenes (Spy) Cas9 nickase containing an N863A mutation (Cas9n), a peptide linker selected from Table 10 (Linker), and a reverse transcriptase domain of retroviral origin selected from Table 6 (RT). FIG. 2B provides a schematic of the screen conducted with the pooled elements from the library of gene modifying polypeptide candidates.

FIG. 3 provides a schematic of an assay for detecting gene editing, including the target reporter gene (BFP) in the test cell line and the three outcomes in the assay depending on whether there is no edit, an imperfect edit, or a perfect edit of a C to a T, resulting in expression and detecting of GFP rather than BFP.

FIGS. 4A-4C are a series of graphs depicting editing activity of two exemplary gene modifying polypeptides, MLVMS and MMTVB. FIG. 4A shows the editing activity of the two exemplary gene modifying polypeptides as assessed by percent of total cells converted to GFP-positive. FIG. 4B shows the editing activity of the two exemplary gene modifying polypeptides in the screen of Examples 2 and 3. FIG. 4C shows violin plots of the editing activities of all the exemplary gene modifying polypeptides comprising RT domains of the MLVMS RT family and of the MMTVB RT family.

FIGS. 5A-5G provide violin plots showing enrichment of exemplary gene modifying polypeptides grouped by RT family. FIG. 5A shows violin plots of enrichment after HEK293T cells were treated with the gene modifying polypeptide and exemplary template RNA g4. FIG. 5B shows violin plots of enrichment after U2OS cells were treated with the gene modifying polypeptide and exemplary template RNA g4. FIG. 5C shows violin plots of enrichment after HEK293T cells were treated with the gene modifying polypeptide and exemplary template RNA g10. FIG. 5D shows violin plots of enrichment after U2OS cells were treated with the gene modifying polypeptide and exemplary template RNA g10. FIG. 5E shows data for an additional replicate of the data presented in FIG. 5A, where HEK293T cells were treated with the gene modifying polypeptide and exemplary template RNA g4. FIG. 5F shows data for a further additional replicate of the data presented in FIG. 5A, where HEK293T cells were treated with the gene modifying polypeptide and exemplary template RNA g4. FIG. 5G shows violin plots combining the data of FIGS. 5A, 5E, and 5F, where HEK293T cells were treated with the gene modifying polypeptide and exemplary template RNA g4.

FIG. 6 shows a graph of enrichment of exemplary gene modifying polypeptides when editing activity was tested in HEK293T cells (X-axis) or in U2OS cells (Y-axis). A linear regression line is plotted based upon the scatter plot data.

FIG. 7 shows a graph of enrichment of exemplary gene modifying polypeptides when editing activity was tested with exemplary template RNA g4 (X-axis) or with exemplary template RNA g10 (Y-axis). A linear regression line is plotted based upon the scatter plot data.

FIGS. 8A-8F provide violin plots showing enrichment of exemplary gene modifying polypeptides grouped by RT family (FIG. 8A MLVAV, FIG. 8B MLVBM, FIG. 8C BAEVM, FIG. 8D FLV, FIG. 8E, FOAMV, FIG. 8F GALV), where the wild-type RT family gene modifying polypeptide is given at left, followed at right by gene modifying polypeptides comprising an increasing number of substitution mutations.

FIGS. 9A-9H provide violin plots showing enrichment of exemplary gene modifying polypeptides grouped by RT family (FIG. 9A KORV, FIG. 9B AVIRE, FIG. 9C MLVCB, FIG. 9D MLVFF, FIG. 9E MLVMS, FIG. 9F SFV3L, FIG. 9G WMSV, FIG. 9H XMRV6), where the wild-type RT family gene modifying polypeptide is given at left, followed at right by gene modifying polypeptides comprising an increasing number of substitution mutations. For KORV and SFV3L RT families, variants deleting/disabling the protease domain of the RT domain were also evaluated.

FIGS. 10A-10C provide violin plots showing enrichment of exemplary gene modifying polypeptides grouped by RT family (FIG. 10A PERV, FIG. 10B SFV1, FIG. 10C FFV), where the wild-type RT family gene modifying polypeptide is given at left, followed at right by gene modifying polypeptides comprising an increasing number of substitution mutations. For SFV1 and FFV RT families, variants deleting/disabling the protease domain of the RT domain were also evaluated.

FIG. 11 provides box and whisker graphs of enrichment of a selection of exemplary gene modifying polypeptides grouped by linker, where the square dotted line indicates the average enrichment of gene modifying polypeptides comprising the top performing linker and the dashed dotted lines indicate the standard error of the mean around said average enrichment. Figure discloses SEQ ID NOS 5217, 5130, 5006, 5129, 5128, 5124, 5112, 5220, 5136, 5219, 5118, 5143-5144, 5116, 5114-5115, 5117 and 5138, respectively, in order of appearance.

FIGS. 12A-12D show graphs of editing activity of exemplary gene modifying polypeptides when editing is targeted to a genomic landing pad BFP gene in U2OS cells (FIG. 12A), when editing is targeted to HEK3 in U2OS cells (FIG. 12B), when editing is targeted to murine Fah in primary murine hepatocytes (FIG. 12C), and when editing is targeted to murine Fah in the liver of Fah5981SB model mice (FIG. 12D).

FIG. 13 shows a graph of enrichment of a selection of exemplary gene modifying polypeptides after being provided to cells as a plasmid (DNA) or as mRNA.

FIG. 14 is a graph showing the Z-scores of a library of gene modifying polypeptide candidates in each of three conditions.

FIG. 15 is a diagram showing a workflow for arrayed screening of gene modifying polypeptides using flow cytometry.

FIG. 16 is a series of graphs showing the percentage of cells undergoing to a successful rewriting event and exhibiting GFP fluorescence after introduction of a gene modifying polypeptide and a plasmid according to the workflow shown in FIG. 15 .

FIG. 17 is a series of graphs showing the result of testing of arrayed lead candidates compared to the results from screening pooled RT candidates.

DETAILED DESCRIPTION Definitions

The term “expression cassette,” as used herein, refers to a nucleic acid construct comprising nucleic acid elements sufficient for the expression of the nucleic acid molecule of the instant invention.

A “gRNA spacer,” as used herein, refers to a portion of a nucleic acid that has complementarity to a target nucleic acid and can, together with a gRNA scaffold, target a Cas protein to the target nucleic acid.

A “gRNA scaffold,” as used herein, refers to a portion of a nucleic acid that can bind a Cas protein and can, together with a gRNA spacer, target the Cas protein to the target nucleic acid. In some embodiments, the gRNA scaffold comprises a crRNA sequence, tetraloop, and tracrRNA sequence.

A “gene modifying polypeptide,” as used herein, refers to a polypeptide comprising a retroviral reverse transcriptase, or a polypeptide comprising an amino acid sequence having at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% amino acid sequence identity to a retroviral reverse transcriptase, which is capable of integrating a nucleic acid sequence (e.g., a sequence provided on a template nucleic acid) into a target DNA molecule (e.g., in a mammalian host cell, such as a genomic DNA molecule in the host cell). In some embodiments, the gene modifying polypeptide is capable of integrating the sequence substantially without relying on host machinery. In some embodiments, the gene modifying polypeptide integrates a sequence into a random position in a genome, and in some embodiments, the gene modifying polypeptide integrates a sequence into a specific target site. In some embodiments, a gene modifying polypeptide includes one or more domains that, collectively, facilitate 1) binding the template nucleic acid, 2) binding the target DNA molecule, and 3) facilitate integration of the at least a portion of the template nucleic acid into the target DNA. Gene modifying polypeptides include both naturally occurring polypeptides as well as engineered variants of the foregoing, e.g., having one or more amino acid substitutions to the naturally occurring sequence. Gene modifying polypeptides also include heterologous constructs, e.g., where one or more of the domains recited above are heterologous to each other, whether through a heterologous fusion (or other conjugate) of otherwise wild-type domains, as well as fusions of modified domains, e.g., by way of replacement or fusion of a heterologous sub-domain or other substituted domain. Exemplary gene modifying polypeptides, and systems comprising them and methods of using them, that can be used in the methods provided herein are described, e.g., in PCT/US2021/020948, which is incorporated herein by reference with respect to gene modifying polypeptides that comprise a retroviral reverse transcriptase domain. In some embodiments, a gene modifying polypeptide integrates a sequence into a gene. In some embodiments, a gene modifying polypeptide integrates a sequence into a sequence outside of a gene. A “gene modifying system,” as used herein, refers to a system comprising a gene modifying polypeptide and a template nucleic acid.

The term “domain” as used herein refers to a structure of a biomolecule that contributes to a specified function of the biomolecule. A domain may comprise a contiguous region (e.g., a contiguous sequence) or distinct, non-contiguous regions (e.g., non-contiguous sequences) of a biomolecule. Examples of protein domains include, but are not limited to, an endonuclease domain, a DNA binding domain, a reverse transcription domain; an example of a domain of a nucleic acid is a regulatory domain, such as a transcription factor binding domain. In some embodiments, a domain (e.g., a Cas domain) can comprise two or more smaller domains (e.g., a DNA binding domain and an endonuclease domain).

As used herein, the term “exogenous,” when used with reference to a biomolecule (such as a nucleic acid sequence or polypeptide) means that the biomolecule was introduced into a host genome, cell or organism by the hand of man. For example, a nucleic acid that is as added into an existing genome, cell, tissue or subject using recombinant DNA techniques or other methods is exogenous to the existing nucleic acid sequence, cell, tissue or subject.

As used herein, “first strand” and “second strand,” as used to describe the individual DNA strands of target DNA, distinguish the two DNA strands based upon which strand the reverse transcriptase domain initiates polymerization, e.g., based upon where target primed synthesis initiates. The first strand refers to the strand of the target DNA upon which the reverse transcriptase domain initiates polymerization, e.g., where target primed synthesis initiates. The second strand refers to the other strand of the target DNA. First and second strand designations do not describe the target site DNA strands in other respects; for example, in some embodiments the first and second strands are nicked by a polypeptide described herein, but the designations ‘first’ and ‘second’ strand have no bearing on the order in which such nicks occur.

A “genomic safe harbor site” (GSH site) is a site in a host genome that is able to accommodate the integration of new genetic material, e.g., such that the inserted genetic element does not cause significant alterations of the host genome posing a risk to the host cell or organism. A GSH site generally meets 1, 2, 3, 4, 5, 6, 7, 8 or 9 of the following criteria: (i) is located >300 kb from a cancer-related gene; (ii) is >300 kb from a miRNA/other functional small RNA; (iii) is >50 kb from a 5′ gene end; (iv) is >50 kb from a replication origin; (v) is >50 kb away from any ultraconservered element; (vi) has low transcriptional activity (i.e. no mRNA+/−25 kb); (vii) is not in a copy number variable region; (viii) is in open chromatin; and/or (ix) is unique, with 1 copy in the human genome. Examples of GSH sites in the human genome that meet some or all of these criteria include (i) the adeno-associated virus site 1 (AAVS1), a naturally occurring site of integration of AAV virus on chromosome 19; (ii) the chemokine (C—C motif) receptor 5 (CCR5) gene, a chemokine receptor gene known as an HIV-1 coreceptor; (iii) the human ortholog of the mouse Rosa26 locus; (iv) the ribosomal DNA (“rDNA”) locus. Additional GSH sites are known and described, e.g., in Pellenz et al. epub Aug. 20, 2018 (doi.org/10.1101/396390).

The term “heterologous,” as used herein to describe a first element in reference to a second element means that the first element and second element do not exist in nature disposed as described. For example, a heterologous polypeptide, nucleic acid molecule, construct or sequence refers to (a) a polypeptide, nucleic acid molecule or portion of a polypeptide or nucleic acid molecule sequence that is not native to a cell in which it is expressed, (b) a polypeptide or nucleic acid molecule or portion of a polypeptide or nucleic acid molecule that has been altered or mutated relative to its native state, or (c) a polypeptide or nucleic acid molecule with an altered expression as compared to the native expression levels under similar conditions. For example, a heterologous regulatory sequence (e.g., promoter, enhancer) may be used to regulate expression of a gene or a nucleic acid molecule in a way that is different than the gene or a nucleic acid molecule is normally expressed in nature. In another example, a heterologous domain of a polypeptide or nucleic acid sequence (e.g., a DNA binding domain of a polypeptide or nucleic acid encoding a DNA binding domain of a polypeptide) may be disposed relative to other domains or may be a different sequence or from a different source, relative to other domains or portions of a polypeptide or its encoding nucleic acid. In certain embodiments, a heterologous nucleic acid molecule may exist in a native host cell genome, but may have an altered expression level or have a different sequence or both. In other embodiments, heterologous nucleic acid molecules may not be endogenous to a host cell or host genome but instead may have been introduced into a host cell by transformation (e.g., transfection, electroporation), wherein the added molecule may integrate into the host genome or can exist as extra-chromosomal genetic material either transiently (e.g., mRNA) or semi-stably for more than one generation (e.g., episomal viral vector, plasmid or other self-replicating vector).

As used herein, “insertion” of a sequence into a target site refers to the net addition of DNA sequence at the target site, e.g., where there are new nucleotides in the heterologous object sequence with no cognate positions in the unedited target site. In some embodiments, a nucleotide alignment of the PBS sequence and heterologous object sequence to the target nucleic acid sequence would result in an alignment gap in the target nucleic acid sequence.

As used herein, a “deletion” generated by a heterologous object sequence in a target site refers to the net deletion of DNA sequence at the target site, e.g., where there are nucleotides in the unedited target site with no cognate positions in the heterologous object sequence. In some embodiments, a nucleotide alignment of the PBS sequence and heterologous object sequence to the target nucleic acid sequence would result in an alignment gap in the molecule comprising the PBS sequence and heterologous object sequence.

The term “inverted terminal repeats” or “ITRs” as used herein refers to AAV viral cis-elements named so because of their symmetry. These elements promote efficient multiplication of an AAV genome. It is hypothesized that the minimal elements for ITR function are a Rep-binding site (RBS; 5′-GCGCGCTCGCTCGCTC-3′ for AAV2; SEQ ID NO: 4601) and a terminal resolution site (TRS; 5′-AGTTGG-3′ for AAV2) plus a variable palindromic sequence allowing for hairpin formation. According to the present invention, an ITR comprises at least these three elements (RBS, TRS, and sequences allowing the formation of a hairpin). In addition, in the present invention, the term “ITR” refers to ITRs of known natural AAV serotypes (e.g. ITR of a serotype 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or 11 AAV), to chimeric ITRs formed by the fusion of ITR elements derived from different serotypes, and to functional variants thereof “Functional variant” refers to a sequence presenting a sequence identity of at least 80%, 85%, 90%, preferably of at least 95% with a known ITR and allowing multiplication of the sequence that includes said ITR in the presence of Rep proteins.

The term “mutation region,” as used herein, refers to a region in a template RNA having one or more sequence difference relative to the corresponding sequence in a target nucleic acid. The sequence difference may comprise, for example, a substitution, insertion, frameshift, or deletion.

The term “mutated” when applied to nucleic acid sequences means that nucleotides in a nucleic acid sequence are inserted, deleted, or changed compared to a reference (e.g., native) nucleic acid sequence. A single alteration may be made at a locus (a point mutation), or multiple nucleotides may be inserted, deleted, or changed at a single locus. In addition, one or more alterations may be made at any number of loci within a nucleic acid sequence. A nucleic acid sequence may be mutated by any method known in the art.

“Nucleic acid molecule” refers to both RNA and DNA molecules including, without limitation, complementary DNA (“cDNA”), genomic DNA (“gDNA”), and messenger RNA (“mRNA”), and also includes synthetic nucleic acid molecules, such as those that are chemically synthesized or recombinantly produced, such as RNA templates, as described herein. The nucleic acid molecule can be double-stranded or single-stranded, circular, or linear. If single-stranded, the nucleic acid molecule can be the sense strand or the antisense strand. Unless otherwise indicated, and as an example for all sequences described herein under the general format “SEQ ID NO:” “nucleic acid comprising SEQ ID NO: 1” refers to a nucleic acid, at least a portion which has either (i) the sequence of SEQ ID NO: 1, or (ii) a sequence complimentary to SEQ ID NO: 1. The choice between the two is dictated by the context in which SEQ ID NO:1 is used. For instance, if the nucleic acid is used as a probe, the choice between the two is dictated by the requirement that the probe be complementary to the desired target. Nucleic acid sequences of the present disclosure may be modified chemically or biochemically or may contain non-natural or derivatized nucleotide bases, as will be readily appreciated by those of skill in the art. Such modifications include, for example, labels, methylation, substitution of one or more naturally occurring nucleotides with an analog, inter-nucleotide modifications such as uncharged linkages (for example, methyl phosphonates, phosphotriesters, phosphoramidates, carbamates, etc.), charged linkages (for example, phosphorothioates, phosphorodithioates, etc.), pendant moieties, (for example, polypeptides), intercalators (for example, acridine, psoralen, etc.), chelators, alkylators, and modified linkages (for example, alpha anomeric nucleic acids, etc.). Also included are chemically modified bases (see, for example, Table 13, infra), backbones (see, for example, Table 14, infra), and modified caps (see, for example, Table 15, infra). Also included are synthetic molecules that mimic polynucleotides in their ability to bind to a designated sequence via hydrogen bonding and other chemical interactions. Such molecules are known in the art and include, for example, those in which peptide linkages substitute for phosphate linkages in the backbone of a molecule, e.g., peptide nucleic acids (PNAs). Other modifications can include, for example, analogs in which the ribose ring contains a bridging moiety or other structure such as modifications found in “locked” nucleic acids (LNAs). In various embodiments, the nucleic acids are in operative association with additional genetic elements, such as tissue-specific expression-control sequence(s) (e.g., tissue-specific promoters and tissue-specific microRNA recognition sequences), as well as additional elements, such as inverted repeats (e.g., inverted terminal repeats, such as elements from or derived from viruses, e.g., AAV ITRs) and tandem repeats, inverted repeats/direct repeats, homology regions (segments with various degrees of homology to a target DNA), untranslated regions (UTRs) (5′, 3′, or both 5′ and 3′ UTRs), and various combinations of the foregoing. The nucleic acid elements of the systems provided by the invention can be provided in a variety of topologies, including single-stranded, double-stranded, circular, linear, linear with open ends, linear with closed ends, and particular versions of these, such as doggybone DNA (dbDNA), closed-ended DNA (ceDNA).

As used herein, a “gene expression unit” is a nucleic acid sequence comprising at least one regulatory nucleic acid sequence operably linked to at least one effector sequence. A first nucleic acid sequence is operably linked with a second nucleic acid sequence when the first nucleic acid sequence is placed in a functional relationship with the second nucleic acid sequence. For instance, a promoter or enhancer is operably linked to a coding sequence if the promoter or enhancer affects the transcription or expression of the coding sequence. Operably linked DNA sequences may be contiguous or non-contiguous. Where necessary to join two protein-coding regions, operably linked sequences may be in the same reading frame.

The terms “host genome” or “host cell,” as used herein, refer to a cell and/or its genome into which protein and/or genetic material has been introduced. It should be understood that such terms are intended to refer not only to the particular subject cell and/or genome, but to the progeny of such a cell and/or the genome of the progeny of such a cell. Because certain modifications may occur in succeeding generations due to either mutation or environmental influences, such progeny may not, in fact, be identical to the parent cell, but are still included within the scope of the term “host cell” as used herein. A host genome or host cell may be an isolated cell or cell line grown in culture, or genomic material isolated from such a cell or cell line, or may be a host cell or host genome which composing living tissue or an organism. In some instances, a host cell may be an animal cell or a plant cell, e.g., as described herein. In certain instances, a host cell may be a mammalian cell, a human cell, avian cell, reptilian cell, bovine cell, horse cell, pig cell, goat cell, sheep cell, chicken cell, or turkey cell. In certain instances, a host cell may be a corn cell, soy cell, wheat cell, or rice cell.

As used herein, “operative association” describes a functional relationship between two nucleic acid sequences, such as a 1) promoter and 2) a heterologous object sequence, and means, in such example, the promoter and heterologous object sequence (e.g., a gene of interest) are oriented such that, under suitable conditions, the promoter drives expression of the heterologous object sequence. For instance, a template nucleic acid carrying a promoter and a heterologous object sequence may be single-stranded, e.g., either the (+) or (−) orientation. An “operative association” between the promoter and the heterologous object sequence in this template means that, regardless of whether the template nucleic acid will be transcribed in a particular state, when it is in the suitable state (e.g., is in the (+) orientation, in the presence of required catalytic factors, and NTPs, etc.), it is accurately transcribed. Operative association applies analogously to other pairs of nucleic acids, including other tissue-specific expression control sequences (such as enhancers, repressors and microRNA recognition sequences), IR/DR, ITRs, UTRs, or homology regions and heterologous object sequences or sequences encoding a retroviral RT domain.

As used herein, a “stem-loop sequence” refers to a nucleic acid sequence (e.g., RNA sequence) with sufficient self-complementarity to form a stem-loop, e.g., having a stem comprising at least two (e.g., 3, 4, 5, 6, 7, 8, 9, or 10) base pairs, and a loop with at least three (e.g., four) base pairs. The stem may comprise mismatches or bulges.

As used herein, a “tissue-specific expression-control sequence” means nucleic acid elements that increase or decrease the level of a transcript comprising the heterologous object sequence in a target tissue in a tissue-specific manner, e.g., preferentially in on-target tissue(s), relative to off-target tissue(s). In some embodiments, a tissue-specific expression-control sequence preferentially drives or represses transcription, activity, or the half-life of a transcript comprising the heterologous object sequence in the target tissue in a tissue-specific manner, e.g., preferentially in an on-target tissue(s), relative to an off-target tissue(s). Exemplary tissue-specific expression-control sequences include tissue-specific promoters, repressors, enhancers, or combinations thereof, as well as tissue-specific microRNA recognition sequences. Tissue specificity refers to on-target (tissue(s) where expression or activity of the template nucleic acid is desired or tolerable) and off-target (tissue(s) where expression or activity of the template nucleic acid is not desired or is not tolerable). For example, a tissue-specific promoter drives expression preferentially in on-target tissues, relative to off-target tissues. In contrast, a microRNA that binds the tissue-specific microRNA recognition sequences is preferentially expressed in off-target tissues, relative to on-target tissues, thereby reducing expression of a template nucleic acid in off-target tissues. Accordingly, a promoter and a microRNA recognition sequence that are specific for the same tissue, such as the target tissue, have contrasting functions (promote and repress, respectively, with concordant expression levels, i.e., high levels of the microRNA in off-target tissues and low levels in on-target tissues, while promoters drive high expression in on-target tissues and low expression in off-target tissues) with regard to the transcription, activity, or half-life of an associated sequence in that tissue.

Table of Contents 1) Introduction 2) Gene modifying systems a) Polypeptide components of gene modifying systems i) Writing domain ii) Endonuclease domains and DNA binding domains (1) Gene modifying polypeptides comprising Cas domains (2) TAL Effectors and Zinc Finger Nucleases iii) Linkers iv) Localization sequences for gene modifying systems v) Evolved Variants of Gene Modifying Polypeptides and Systems vi) Inteins vii) Additional domains b) Template nucleic acids i) gRNA spacer and gRNA scaffold ii) Heterologous object sequence iii) PBS sequence iv) Exemplary Template Sequences c) gRNAs with inducible activity d) Circular RNAs and Ribozymes in Gene Modifying Systems e) Target Nucleic Acid Site f) Second strand nicking 3) Production of Compositions and Systems 4) Therapeutic Applications 5) Administration and Delivery a) Tissue Specific Activity/Administration i) Promoters ii) microRNAs b) Viral vectors and components thereof c) AAV Administration d) Lipid Nanoparticles 6) Kits, Articles of Manufacture, and Pharmaceutical Compositions 7) Chemistry, Manufacturing, and Controls (CMC)

INTRODUCTION

This disclosure relates to methods compositions for targeting, editing, modifying or manipulating a DNA sequence (e.g., inserting a heterologous object sequence into a target site of a mammalian genome) at one or more locations in a DNA sequence in a cell, tissue or subject, e.g., in vivo or in vitro. The heterologous object DNA sequence may include, e.g., a substitution, a deletion, an insertion, e.g., a coding sequence, a regulatory sequence, or a gene expression unit.

The disclosure also provides methods for treating disease using reverse transcriptase-based systems for altering a genomic DNA sequence of interest, e.g., by inserting, deleting, or substituting one or more nucleotides into/from the sequence of interest.

The disclosure provides, in part, methods for treating disease using a gene modifying system comprising a gene modifying polypeptide component and a template nucleic acid (e.g., template RNA) component. In some embodiments, a gene modifying system can be used to introduce an alteration into a target site in a genome. In some embodiments, the gene modifying polypeptide component comprises a writing domain (e.g., a reverse transcriptase domain), a DNA-binding domain, and an endonuclease domain (e.g., nickase domain). In some embodiments, the template nucleic acid (e.g., template RNA) comprises a sequence (e.g., a gRNA spacer) that binds a target site in the genome (e.g., that binds to a second strand of the target site), a sequence (e.g., a gRNA scaffold) that binds the gene modifying polypeptide component, a heterologous object sequence, and a PBS sequence. Without wishing to be bound by theory, it is thought that the template nucleic acid (e.g., template RNA) binds to the second strand of a target site in the genome, and binds to the gene modifying polypeptide component (e.g., localizing the polypeptide component to the target site in the genome). It is thought that the endonuclease (e.g., nickase) of the gene modifying polypeptide component cuts the target site (e.g., the first strand of the target site), e.g., allowing the PBS sequence to bind to a sequence adjacent to the site to be altered on the first strand of the target site. It is thought that the writing domain (e.g., reverse transcriptase domain) of the polypeptide component uses the first strand of the target site that is bound to the complementary sequence comprising the PBS sequence of the template nucleic acid as a primer and the heterologous object sequence of the template nucleic acid as a template to, e.g., polymerize a sequence complementary to the heterologous object sequence. Without wishing to be bound by theory, it is thought that selection of an appropriate heterologous object sequence can result in substitution, deletion, and/or insertion of one or more nucleotides at the target site.

Gene Modifying Systems

In some embodiments, a gene modifying system described herein comprises: (A) a gene modifying polypeptide or a nucleic acid encoding the gene modifying polypeptide, wherein the gene modifying polypeptide comprises (i) a reverse transcriptase domain, and either (x) an endonuclease domain that contains DNA binding functionality or (y) an endonuclease domain and separate DNA binding domain; and (B) a template RNA. A gene modifying polypeptide, in some embodiments, acts as a substantially autonomous protein machine capable of integrating a template nucleic acid sequence into a target DNA molecule (e.g., in a mammalian host cell, such as a genomic DNA molecule in the host cell), substantially without relying on host machinery. For example, the gene modifying protein may comprise a DNA-binding domain, a reverse transcriptase domain, and an endonuclease domain. In some embodiments, the DNA-binding function may involve an RNA component that directs the protein to a DNA sequence, e.g., a gRNA spacer. In other embodiments, the gene modifying polypeptide may comprise a reverse transcriptase domain and an endonuclease domain. The RNA template element of a gene modifying system is typically heterologous to the gene modifying polypeptide element and provides an object sequence to be inserted (reverse transcribed) into the host genome. In some embodiments, the gene modifying polypeptide is capable of target primed reverse transcription. In some embodiments, the gene modifying polypeptide is capable of second-strand synthesis.

In some embodiments the gene modifying system is combined with a second polypeptide. In some embodiments, the second polypeptide may comprise an endonuclease domain. In some embodiments, the second polypeptide may comprise a polymerase domain, e.g., a reverse transcriptase domain. In some embodiments, the second polypeptide may comprise a DNA-dependent DNA polymerase domain. In some embodiments, the second polypeptide aids in completion of the genome edit, e.g., by contributing to second-strand synthesis or DNA repair resolution.

A functional gene modifying polypeptide can be made up of unrelated DNA binding, reverse transcription, and endonuclease domains. This modular structure allows combining of functional domains, e.g., dCas9 (DNA binding), MMLV reverse transcriptase (reverse transcription), FokI (endonuclease). In some embodiments, multiple functional domains may arise from a single protein, e.g., Cas9 or Cas9 nickase (DNA binding, endonuclease).

In some embodiments, a gene modifying polypeptide includes one or more domains that, collectively, facilitate 1) binding the template nucleic acid, 2) binding the target DNA molecule, and 3) facilitate integration of the at least a portion of the template nucleic acid into the target DNA. In some embodiments, the gene modifying polypeptide is an engineered polypeptide that comprises one or more amino acid substitutions to a corresponding naturally occurring sequence. In some embodiments, the gene modifying polypeptide comprises two or more domains that are heterologous relative to each other, e.g., through a heterologous fusion (or other conjugate) of otherwise wild-type domains, or well as fusions of modified domains, e.g., by way of replacement or fusion of a heterologous sub-domain or other substituted domain. For instance, in some embodiments, one or more of: the RT domain is heterologous to the DBD; the DBD is heterologous to the endonuclease domain; or the RT domain is heterologous to the endonuclease domain.

In some embodiments, a template RNA molecule for use in the system comprises, from 5′ to 3′ (1) a gRNA spacer; (2) a gRNA scaffold; (3) heterologous object sequence (4) a primer binding site (PBS) sequence. In some embodiments:

-   -   (1) Is a gRNA spacer of ˜18-22 nt, e.g., is 20 nt     -   (2) Is a gRNA scaffold comprising one or more hairpin loops,         e.g., 1, 2, of 3 loops for associating the template with a Cas         domain, e.g., a nickase Cas9 domain. In some embodiments, the         gRNA scaffold comprises the sequence, from 5′ to 3′,

(SEQ ID NO: 5008) GTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGTCCGTTATC AACTTGAAAAAGTGGGACCGAGTCGGTCC.

-   -   (3) In some embodiments, the heterologous object sequence is,         e.g., 7-74, e.g., 10-20, 20-30, 30-40, 40-50, 50-60, 60-70, or         70-80 nt or, 80-90 nt in length. In some embodiments, the first         (most 5′) base of the sequence is not C.     -   (4) In some embodiments, the PBS sequence that binds the target         priming sequence after nicking occurs is e.g., 3-20 nt, e.g.,         7-15 nt, e.g., 12-14 nt. In some embodiments, the PBS sequence         has 40-60% GC content.

In some embodiments, a second gRNA associated with the system may help drive complete integration. In some embodiments, the second gRNA may target a location that is 0-200 nt away from the first-strand nick, e.g., 0-50, 50-100, 100-200 nt away from the first-strand nick. In some embodiments, the second gRNA can only bind its target sequence after the edit is made, e.g., the gRNA binds a sequence present in the heterologous object sequence, but not in the initial target sequence.

In some embodiments, a gene modifying system described herein is used to make an edit in HEK293, K562, U2OS, or HeLa cells. In some embodiment, a gene modifying system is used to make an edit in primary cells, e.g., primary cortical neurons from E18.5 mice.

In some embodiments, a gene modifying polypeptide as described herein comprises a reverse transcriptase or RT domain (e.g., as described herein) that comprises a MoMLV RT sequence or variant thereof. In embodiments, the MoMLV RT sequence comprises one or more mutations selected from D200N, L603W, T330P, T306K, W313F, D524G, E562Q, D583N, P51L, S67R, E67K, T197A, H204R, E302K, F309N, L435G, N454K, H594Q, D653N, R110S, and K103L. In embodiments, the MoMLV RT sequence comprises a combination of mutations, such as D200N, L603W, and T330P, optionally further including T306K and/or W313F.

In some embodiments, an endonuclease domain (e.g., as described herein) comprises nCAS9, e.g., comprising the H840A mutation.

In some embodiments, the heterologous object sequence (e.g., of a system as described herein) is about 1-50, 50-100, 100-200, 200-300, 300-400, 400-500, 500-600, 600-700, 700-800, 800-900, 900-1000, or more, nucleotides in length.

In some embodiments, the RT and endonuclease domains are joined by a flexible linker, e.g., comprising the amino acid sequence SGGSSGGSSGSETPGTSESATPESSGGSSGGSS (SEQ ID NO: 5006).

In some embodiments, the endonuclease domain is N-terminal relative to the RT domain. In some embodiments, the endonuclease domain is C-terminal relative to the RT domain.

In some embodiments, the system incorporates a heterologous object sequence into a target site by TPRT, e.g., as described herein.

In some embodiments, a gene modifying polypeptide comprises a DNA binding domain. In some embodiments, a gene modifying polypeptide comprises an RNA binding domain. In some embodiments, the RNA binding domain comprises an RNA binding domain of B-box protein, MS2 coat protein, dCas, or an element of a sequence of a table herein. In some embodiments, the RNA binding domain is capable of binding to a template RNA with greater affinity than a reference RNA binding domain.

In some embodiments, a gene modifying system is capable of producing an insertion into the target site of at least 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100 nucleotides (and optionally no more than 500, 400, 300, 200, or 100 nucleotides). In some embodiments, a gene modifying system is capable of producing an insertion into the target site of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100 nucleotides (and optionally no more than 500, 400, 300, 200, or 100 nucleotides). In some embodiments, a gene modifying system is capable of producing an insertion into the target site of at least 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 5.5, 6, 6.5, 7, 7.5, 8, 8.5, 9, 9.5 or 10 kilobases (and optionally no more than 1, 5, 10, or 20 kilobases). In some embodiments, a gene modifying system is capable of producing a deletion of at least 81, 85, 90, 95, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, or 200 nucleotides (and optionally no more than 500, 400, 300, or 200 nucleotides). In some embodiments, a gene modifying system is capable of producing a deletion of at least 81, 85, 90, 95, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, or 200 nucleotides (and optionally no more than 500, 400, 300, or 200 nucleotides). In some embodiments, a gene modifying system is capable of producing a deletion of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, or 200 nucleotides (and optionally no more than 500, 400, 300, or 200 nucleotides). In some embodiments, a gene modifying system is capable of producing a deletion of at least 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 5.5, 6, 6.5, 7, 7.5, 8, 8.5, 9, 9.5 or 10 kilobases (and optionally no more than 1, 5, 10, or 20 kilobases). In some embodiments, a gene modifying system is capable of producing a substitution into the target site of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, or 100 or more nucleotides. In some embodiments, a gene modifying system is capable of producing a substitution in the target site of 1-2, 2-3, 3-4, 4-5, 5-10, 10-15, 15-20, 20-30, 30-40, 40-50, 50-60, 60-70, 70-80, 80-90, or 90-100 nucleotides.

In some embodiments, the substitution is a transition mutation. In some embodiments, the substitution is a transversion mutation. In some embodiments, the substitution converts an adenine to a thymine, an adenine to a guanine, an adenine to a cytosine, a guanine to a thymine, a guanine to a cytosine, a guanine to an adenine, a thymine to a cytosine, a thymine to an adenine, a thymine to a guanine, a cytosine to an adenine, a cytosine to a guanine, or a cytosine to a thymine.

In some embodiments, an insertion, deletion, substitution, or combination thereof, increases or decreases expression (e.g. transcription or translation) of a gene. In some embodiments, an insertion, deletion, substitution, or combination thereof, increases or decreases expression (e.g. transcription or translation) of a gene by altering, adding, or deleting sequences in a promoter or enhancer, e.g. sequences that bind transcription factors. In some embodiments, an insertion, deletion, substitution, or combination thereof alters translation of a gene (e.g. alters an amino acid sequence), inserts or deletes a start or stop codon, alters or fixes the translation frame of a gene. In some embodiments, an insertion, deletion, substitution, or combination thereof alters splicing of a gene, e.g. by inserting, deleting, or altering a splice acceptor or donor site. In some embodiments, an insertion, deletion, substitution, or combination thereof alters transcript or protein half-life. In some embodiments, an insertion, deletion, substitution, or combination thereof alters protein localization in the cell (e.g. from the cytoplasm to a mitochondria, from the cytoplasm into the extracellular space (e.g. adds a secretion tag)). In some embodiments, an insertion, deletion, substitution, or combination thereof alters (e.g. improves) protein folding (e.g. to prevent accumulation of misfolded proteins). In some embodiments, an insertion, deletion, substitution, or combination thereof, alters, increases, decreases the activity of a gene, e.g. a protein encoded by the gene.

Exemplary gene modifying polypeptides, and systems comprising them and methods of using them are described, e.g., in PCT/US2021/020948, which is incorporated herein by reference with respect to retroviral RT domains, including the amino acid and nucleic acid sequences therein.

Exemplary gene modifying polypeptides and retroviral RT domain sequences are also described, e.g., in International Application No. PCT/US21/20948 filed Mar. 4, 2021, e.g., at Table 30, Table 31, and Table 44 therein; the entire application is incorporated by reference herein with respect to retroviral RTs, e.g., in said sequences and tables. Accordingly, a gene modifying polypeptide described herein may comprise an amino acid sequence according to any of the Tables mentioned in this paragraph, or a domain thereof (e.g., a retroviral RT domain), or a functional fragment or variant of any of the foregoing, or an amino acid sequence having at least 70%, 80%, 85%, 90%, 95%, or 99% identity thereto.

In some embodiments, a polypeptide for use in any of the systems described herein can be a molecular reconstruction or ancestral reconstruction based upon the aligned polypeptide sequence of multiple homologous proteins. In some embodiments, a reverse transcriptase domain for use in any of the systems described herein can be a molecular reconstruction or an ancestral reconstruction, or can be modified at particular residues, based upon alignments of reverse transcriptase domains from the same or different sources. A skilled artisan can, based on the Accession numbers provided herein, align polypeptides or nucleic acid sequences, e.g., by using routine sequence analysis tools as Basic Local Alignment Search Tool (BLAST) or CD-Search for conserved domain analysis. Molecular reconstructions can be created based upon sequence consensus, e.g. using approaches described in Ivics et al., Cell 1997, 501-510; Wagstaff et al., Molecular Biology and Evolution 2013, 88-99.

Polypeptide Components of Gene Modifying Systems

In some embodiments, the gene modifying polypeptide possesses the functions of DNA target site binding, template nucleic acid (e.g., RNA) binding, DNA target site cleavage, and template nucleic acid (e.g., RNA) writing, e.g., reverse transcription. In some embodiments, each function is contained within a distinct domain. In some embodiments, a function may be attributed to two or more domains (e.g., two or more domains, together, exhibit the functionality). In some embodiments, two or more domains may have the same or similar function (e.g., two or more domains each independently have DNA-binding functionality, e.g., for two different DNA sequences). In other embodiments, one or more domains may be capable of enabling one or more functions, e.g., a Cas9 domain enabling both DNA binding and target site cleavage. In some embodiments, the domains are all located within a single polypeptide. In some embodiments, a first domain is in one polypeptide and a second domain is in a second polypeptide. For example, in some embodiments, the sequences may be split between a first polypeptide and a second polypeptide, e.g., wherein the first polypeptide comprises a reverse transcriptase (RT) domain and wherein the second polypeptide comprises a DNA-binding domain and an endonuclease domain, e.g., a nickase domain. As a further example, in some embodiments, the first polypeptide and the second polypeptide each comprise a DNA binding domain (e.g., a first DNA binding domain and a second DNA binding domain). In some embodiments, the first and second polypeptide may be brought together post-translationally via a split-intein to form a single gene modifying polypeptide.

In an aspect, the disclosure provides a gene modifying polypeptide comprising:

-   -   a DNA binding domain (DBD) that binds to a target nucleic acid         sequence,     -   the RT domain of an AVIRE RT, or an amino acid sequence having         at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99%         identity thereto, and     -   a linker disposed between the DBD and the RT domain (e.g., a         linker comprising an amino acid sequence as listed in Table 10,         or an amino acid sequence having at least 70%, 75%, 80%, 85%,         90%, 95%, 96%, 97%, 98%, or 99% identity thereto);     -   wherein the DBD is heterologous to the RT domain (e.g., a Cas         domain, e.g., a Cas nickase domain, e.g., a Cas9 nickase         domain); optionally wherein the RT domain is C-terminal of the         Cas domain.

In an aspect, the disclosure provides a gene modifying polypeptide comprising:

-   -   a DNA binding domain (DBD) that binds to a target nucleic acid         sequence,     -   the RT domain of an BAEVM RT, or an amino acid sequence having         at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99%         identity thereto, and     -   a linker disposed between the DBD and the RT domain (e.g., a         linker comprising an amino acid sequence as listed in Table 10,         or an amino acid sequence having at least 70%, 75%, 80%, 85%,         90%, 95%, 96%, 97%, 98%, or 99% identity thereto);     -   wherein the DBD is heterologous to the RT domain (e.g., a Cas         domain, e.g., a Cas nickase domain, e.g., a Cas9 nickase         domain); optionally wherein the RT domain is C-terminal of the         Cas domain.

In an aspect, the disclosure provides a gene modifying polypeptide comprising:

-   -   a DNA binding domain (DBD) that binds to a target nucleic acid         sequence,     -   the RT domain of an FFV RT, or an amino acid sequence having at         least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99%         identity thereto, and     -   a linker disposed between the DBD and the RT domain (e.g., a         linker comprising an amino acid sequence as listed in Table 10,         or an amino acid sequence having at least 70%, 75%, 80%, 85%,         90%, 95%, 96%, 97%, 98%, or 99% identity thereto);     -   wherein the DBD is heterologous to the RT domain (e.g., a Cas         domain, e.g., a Cas nickase domain, e.g., a Cas9 nickase         domain); optionally wherein the RT domain is C-terminal of the         Cas domain.

In an aspect, the disclosure provides a gene modifying polypeptide comprising:

-   -   a DNA binding domain (DBD) that binds to a target nucleic acid         sequence,     -   the RT domain of an FLV RT, or an amino acid sequence having at         least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99%         identity thereto, and     -   a linker disposed between the DBD and the RT domain (e.g., a         linker comprising an amino acid sequence as listed in Table 10,         or an amino acid sequence having at least 70%, 75%, 80%, 85%,         90%, 95%, 96%, 97%, 98%, or 99% identity thereto);     -   wherein the DBD is heterologous to the RT domain (e.g., a Cas         domain, e.g., a Cas nickase domain, e.g., a Cas9 nickase         domain); optionally wherein the RT domain is C-terminal of the         Cas domain.

In an aspect, the disclosure provides a gene modifying polypeptide comprising:

-   -   a DNA binding domain (DBD) that binds to a target nucleic acid         sequence,     -   the RT domain of an FOAMV RT, or an amino acid sequence having         at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99%         identity thereto, and     -   a linker disposed between the DBD and the RT domain (e.g., a         linker comprising an amino acid sequence as listed in Table 10,         or an amino acid sequence having at least 70%, 75%, 80%, 85%,         90%, 95%, 96%, 97%, 98%, or 99% identity thereto);     -   wherein the DBD is heterologous to the RT domain (e.g., a Cas         domain, e.g., a Cas nickase domain, e.g., a Cas9 nickase         domain); optionally wherein the RT domain is C-terminal of the         Cas domain.

In an aspect, the disclosure provides a gene modifying polypeptide comprising:

-   -   a DNA binding domain (DBD) that binds to a target nucleic acid         sequence,     -   the RT domain of an GALV RT, or an amino acid sequence having at         least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99%         identity thereto, and     -   a linker disposed between the DBD and the RT domain (e.g., a         linker comprising an amino acid sequence as listed in Table 10,         or an amino acid sequence having at least 70%, 75%, 80%, 85%,         90%, 95%, 96%, 97%, 98%, or 99% identity thereto);     -   wherein the DBD is heterologous to the RT domain (e.g., a Cas         domain, e.g., a Cas nickase domain, e.g., a Cas9 nickase         domain); optionally wherein the RT domain is C-terminal of the         Cas domain.

In an aspect, the disclosure provides a gene modifying polypeptide comprising:

-   -   a DNA binding domain (DBD) that binds to a target nucleic acid         sequence,     -   the RT domain of an KORV RT, or an amino acid sequence having at         least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99%         identity thereto, and     -   a linker disposed between the DBD and the RT domain (e.g., a         linker comprising an amino acid sequence as listed in Table 10,         or an amino acid sequence having at least 70%, 75%, 80%, 85%,         90%, 95%, 96%, 97%, 98%, or 99% identity thereto);     -   wherein the DBD is heterologous to the RT domain (e.g., a Cas         domain, e.g., a Cas nickase domain, e.g., a Cas9 nickase         domain); optionally wherein the RT domain is C-terminal of the         Cas domain.

In an aspect, the disclosure provides a gene modifying polypeptide comprising:

-   -   a DNA binding domain (DBD) that binds to a target nucleic acid         sequence,     -   the RT domain of an MLVAV RT, or an amino acid sequence having         at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99%         identity thereto, and     -   a linker disposed between the DBD and the RT domain (e.g., a         linker comprising an amino acid sequence as listed in Table 10,         or an amino acid sequence having at least 70%, 75%, 80%, 85%,         90%, 95%, 96%, 97%, 98%, or 99% identity thereto);     -   wherein the DBD is heterologous to the RT domain (e.g., a Cas         domain, e.g., a Cas nickase domain, e.g., a Cas9 nickase         domain); optionally wherein the RT domain is C-terminal of the         Cas domain.

In an aspect, the disclosure provides a gene modifying polypeptide comprising:

-   -   a DNA binding domain (DBD) that binds to a target nucleic acid         sequence,     -   the RT domain of an MLVBM RT, or an amino acid sequence having         at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99%         identity thereto, and     -   a linker disposed between the DBD and the RT domain (e.g., a         linker comprising an amino acid sequence as listed in Table 10,         or an amino acid sequence having at least 70%, 75%, 80%, 85%,         90%, 95%, 96%, 97%, 98%, or 99% identity thereto);     -   wherein the DBD is heterologous to the RT domain (e.g., a Cas         domain, e.g., a Cas nickase domain, e.g., a Cas9 nickase         domain); optionally wherein the RT domain is C-terminal of the         Cas domain.

In an aspect, the disclosure provides a gene modifying polypeptide comprising:

-   -   a DNA binding domain (DBD) that binds to a target nucleic acid         sequence,     -   the RT domain of an MLVCB RT, or an amino acid sequence having         at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99%         identity thereto, and     -   a linker disposed between the DBD and the RT domain (e.g., a         linker comprising an amino acid sequence as listed in Table 10,         or an amino acid sequence having at least 70%, 75%, 80%, 85%,         90%, 95%, 96%, 97%, 98%, or 99% identity thereto);     -   wherein the DBD is heterologous to the RT domain (e.g., a Cas         domain, e.g., a Cas nickase domain, e.g., a Cas9 nickase         domain); optionally wherein the RT domain is C-terminal of the         Cas domain.

In an aspect, the disclosure provides a gene modifying polypeptide comprising:

-   -   a DNA binding domain (DBD) that binds to a target nucleic acid         sequence,     -   the RT domain of an MLVFF RT, or an amino acid sequence having         at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99%         identity thereto, and     -   a linker disposed between the DBD and the RT domain (e.g., a         linker comprising an amino acid sequence as listed in Table 10,         or an amino acid sequence having at least 70%, 75%, 80%, 85%,         90%, 95%, 96%, 97%, 98%, or 99% identity thereto);     -   wherein the DBD is heterologous to the RT domain (e.g., a Cas         domain, e.g., a Cas nickase domain, e.g., a Cas9 nickase         domain); optionally wherein the RT domain is C-terminal of the         Cas domain.

In an aspect, the disclosure provides a gene modifying polypeptide comprising:

-   -   a DNA binding domain (DBD) that binds to a target nucleic acid         sequence,     -   the RT domain of an MLVMS RT, or an amino acid sequence having         at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99%         identity thereto, and     -   a linker disposed between the DBD and the RT domain (e.g., a         linker comprising an amino acid sequence as listed in Table 10,         or an amino acid sequence having at least 70%, 75%, 80%, 85%,         90%, 95%, 96%, 97%, 98%, or 99% identity thereto);     -   wherein the DBD is heterologous to the RT domain (e.g., a Cas         domain, e.g., a Cas nickase domain, e.g., a Cas9 nickase         domain); optionally wherein the RT domain is C-terminal of the         Cas domain.

In an aspect, the disclosure provides a gene modifying polypeptide comprising:

-   -   a DNA binding domain (DBD) that binds to a target nucleic acid         sequence,     -   the RT domain of an PERV RT, or an amino acid sequence having at         least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99%         identity thereto, and     -   a linker disposed between the DBD and the RT domain (e.g., a         linker comprising an amino acid sequence as listed in Table 10,         or an amino acid sequence having at least 70%, 75%, 80%, 85%,         90%, 95%, 96%, 97%, 98%, or 99% identity thereto);     -   wherein the DBD is heterologous to the RT domain (e.g., a Cas         domain, e.g., a Cas nickase domain, e.g., a Cas9 nickase         domain); optionally wherein the RT domain is C-terminal of the         Cas domain.

In an aspect, the disclosure provides a gene modifying polypeptide comprising:

-   -   a DNA binding domain (DBD) that binds to a target nucleic acid         sequence,     -   the RT domain of an SFV1 RT, or an amino acid sequence having at         least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99%         identity thereto, and     -   a linker disposed between the DBD and the RT domain (e.g., a         linker comprising an amino acid sequence as listed in Table 10,         or an amino acid sequence having at least 70%, 75%, 80%, 85%,         90%, 95%, 96%, 97%, 98%, or 99% identity thereto);     -   wherein the DBD is heterologous to the RT domain (e.g., a Cas         domain, e.g., a Cas nickase domain, e.g., a Cas9 nickase         domain); optionally wherein the RT domain is C-terminal of the         Cas domain.

In an aspect, the disclosure provides a gene modifying polypeptide comprising:

-   -   a DNA binding domain (DBD) that binds to a target nucleic acid         sequence,     -   the RT domain of an SFV3L RT, or an amino acid sequence having         at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99%         identity thereto, and     -   a linker disposed between the DBD and the RT domain (e.g., a         linker comprising an amino acid sequence as listed in Table 10,         or an amino acid sequence having at least 70%, 75%, 80%, 85%,         90%, 95%, 96%, 97%, 98%, or 99% identity thereto);     -   wherein the DBD is heterologous to the RT domain (e.g., a Cas         domain, e.g., a Cas nickase domain, e.g., a Cas9 nickase         domain); optionally wherein the RT domain is C-terminal of the         Cas domain.

In an aspect, the disclosure provides a gene modifying polypeptide comprising:

-   -   a DNA binding domain (DBD) that binds to a target nucleic acid         sequence,     -   the RT domain of an WMSV RT, or an amino acid sequence having at         least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99%         identity thereto, and     -   a linker disposed between the DBD and the RT domain (e.g., a         linker comprising an amino acid sequence as listed in Table 10,         or an amino acid sequence having at least 70%, 75%, 80%, 85%,         90%, 95%, 96%, 97%, 98%, or 99% identity thereto);     -   wherein the DBD is heterologous to the RT domain (e.g., a Cas         domain, e.g., a Cas nickase domain, e.g., a Cas9 nickase         domain); optionally wherein the RT domain is C-terminal of the         Cas domain.

In an aspect, the disclosure provides a gene modifying polypeptide comprising:

-   -   a DNA binding domain (DBD) that binds to a target nucleic acid         sequence,     -   the RT domain of an XMRV6 RT, or an amino acid sequence having         at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99%         identity thereto, and     -   a linker disposed between the DBD and the RT domain (e.g., a         linker comprising an amino acid sequence as listed in Table 10,         or an amino acid sequence having at least 70%, 75%, 80%, 85%,         90%, 95%, 96%, 97%, 98%, or 99% identity thereto);     -   wherein the DBD is heterologous to the RT domain (e.g., a Cas         domain, e.g., a Cas nickase domain, e.g., a Cas9 nickase         domain); optionally wherein the RT domain is C-terminal of the         Cas domain.

In an aspect, the disclosure provides a gene modifying polypeptide comprising:

-   -   a DNA binding domain (DBD) that binds to a target nucleic acid         sequence,     -   the RT domain of an BLVAU RT, or an amino acid sequence having         at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99%         identity thereto, and     -   a linker disposed between the DBD and the RT domain (e.g., a         linker comprising an amino acid sequence as listed in Table 10,         or an amino acid sequence having at least 70%, 75%, 80%, 85%,         90%, 95%, 96%, 97%, 98%, or 99% identity thereto);     -   wherein the DBD is heterologous to the RT domain (e.g., a Cas         domain, e.g., a Cas nickase domain, e.g., a Cas9 nickase         domain); optionally wherein the RT domain is C-terminal of the         Cas domain.

In an aspect, the disclosure provides a gene modifying polypeptide comprising:

-   -   a DNA binding domain (DBD) that binds to a target nucleic acid         sequence,     -   the RT domain of an BLVJ RT, or an amino acid sequence having at         least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99%         identity thereto, and     -   a linker disposed between the DBD and the RT domain (e.g., a         linker comprising an amino acid sequence as listed in Table 10,         or an amino acid sequence having at least 70%, 75%, 80%, 85%,         90%, 95%, 96%, 97%, 98%, or 99% identity thereto);     -   wherein the DBD is heterologous to the RT domain (e.g., a Cas         domain, e.g., a Cas nickase domain, e.g., a Cas9 nickase         domain); optionally wherein the RT domain is C-terminal of the         Cas domain.

In an aspect, the disclosure provides a gene modifying polypeptide comprising:

-   -   a DNA binding domain (DBD) that binds to a target nucleic acid         sequence,     -   the RT domain of an HTL1A RT, or an amino acid sequence having         at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99%         identity thereto, and     -   a linker disposed between the DBD and the RT domain (e.g., a         linker comprising an amino acid sequence as listed in Table 10,         or an amino acid sequence having at least 70%, 75%, 80%, 85%,         90%, 95%, 96%, 97%, 98%, or 99% identity thereto);     -   wherein the DBD is heterologous to the RT domain (e.g., a Cas         domain, e.g., a Cas nickase domain, e.g., a Cas9 nickase         domain); optionally wherein the RT domain is C-terminal of the         Cas domain.

In an aspect, the disclosure provides a gene modifying polypeptide comprising:

-   -   a DNA binding domain (DBD) that binds to a target nucleic acid         sequence,     -   the RT domain of an HTL1C RT, or an amino acid sequence having         at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99%         identity thereto, and     -   a linker disposed between the DBD and the RT domain (e.g., a         linker comprising an amino acid sequence as listed in Table 10,         or an amino acid sequence having at least 70%, 75%, 80%, 85%,         90%, 95%, 96%, 97%, 98%, or 99% identity thereto);     -   wherein the DBD is heterologous to the RT domain (e.g., a Cas         domain, e.g., a Cas nickase domain, e.g., a Cas9 nickase         domain); optionally wherein the RT domain is C-terminal of the         Cas domain.

In an aspect, the disclosure provides a gene modifying polypeptide comprising:

-   -   a DNA binding domain (DBD) that binds to a target nucleic acid         sequence,     -   the RT domain of an HTL1L RT, or an amino acid sequence having         at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99%         identity thereto, and     -   a linker disposed between the DBD and the RT domain (e.g., a         linker comprising an amino acid sequence as listed in Table 10,         or an amino acid sequence having at least 70%, 75%, 80%, 85%,         90%, 95%, 96%, 97%, 98%, or 99% identity thereto);     -   wherein the DBD is heterologous to the RT domain (e.g., a Cas         domain, e.g., a Cas nickase domain, e.g., a Cas9 nickase         domain); optionally wherein the RT domain is C-terminal of the         Cas domain.

In an aspect, the disclosure provides a gene modifying polypeptide comprising:

-   -   a DNA binding domain (DBD) that binds to a target nucleic acid         sequence,     -   the RT domain of an HTL32 RT, or an amino acid sequence having         at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99%         identity thereto, and     -   a linker disposed between the DBD and the RT domain (e.g., a         linker comprising an amino acid sequence as listed in Table 10,         or an amino acid sequence having at least 70%, 75%, 80%, 85%,         90%, 95%, 96%, 97%, 98%, or 99% identity thereto);     -   wherein the DBD is heterologous to the RT domain (e.g., a Cas         domain, e.g., a Cas nickase domain, e.g., a Cas9 nickase         domain); optionally wherein the RT domain is C-terminal of the         Cas domain.

In an aspect, the disclosure provides a gene modifying polypeptide comprising:

-   -   a DNA binding domain (DBD) that binds to a target nucleic acid         sequence,     -   the RT domain of an HTL3P RT, or an amino acid sequence having         at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99%         identity thereto, and     -   a linker disposed between the DBD and the RT domain (e.g., a         linker comprising an amino acid sequence as listed in Table 10,         or an amino acid sequence having at least 70%, 75%, 80%, 85%,         90%, 95%, 96%, 97%, 98%, or 99% identity thereto);     -   wherein the DBD is heterologous to the RT domain (e.g., a Cas         domain, e.g., a Cas nickase domain, e.g., a Cas9 nickase         domain); optionally wherein the RT domain is C-terminal of the         Cas domain.

In an aspect, the disclosure provides a gene modifying polypeptide comprising:

-   -   a DNA binding domain (DBD) that binds to a target nucleic acid         sequence,     -   the RT domain of an HTLV2 RT, or an amino acid sequence having         at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99%         identity thereto, and     -   a linker disposed between the DBD and the RT domain (e.g., a         linker comprising an amino acid sequence as listed in Table 10,         or an amino acid sequence having at least 70%, 75%, 80%, 85%,         90%, 95%, 96%, 97%, 98%, or 99% identity thereto);     -   wherein the DBD is heterologous to the RT domain (e.g., a Cas         domain, e.g., a Cas nickase domain, e.g., a Cas9 nickase         domain); optionally wherein the RT domain is C-terminal of the         Cas domain.

In an aspect, the disclosure provides a gene modifying polypeptide comprising:

-   -   a DNA binding domain (DBD) that binds to a target nucleic acid         sequence,     -   the RT domain of an JSRV RT, or an amino acid sequence having at         least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99%         identity thereto, and     -   a linker disposed between the DBD and the RT domain (e.g., a         linker comprising an amino acid sequence as listed in Table 10,         or an amino acid sequence having at least 70%, 75%, 80%, 85%,         90%, 95%, 96%, 97%, 98%, or 99% identity thereto);     -   wherein the DBD is heterologous to the RT domain (e.g., a Cas         domain, e.g., a Cas nickase domain, e.g., a Cas9 nickase         domain); optionally wherein the RT domain is C-terminal of the         Cas domain.

In an aspect, the disclosure provides a gene modifying polypeptide comprising:

-   -   a DNA binding domain (DBD) that binds to a target nucleic acid         sequence,     -   the RT domain of an MLVF5 RT, or an amino acid sequence having         at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99%         identity thereto, and     -   a linker disposed between the DBD and the RT domain (e.g., a         linker comprising an amino acid sequence as listed in Table 10,         or an amino acid sequence having at least 70%, 75%, 80%, 85%,         90%, 95%, 96%, 97%, 98%, or 99% identity thereto);     -   wherein the DBD is heterologous to the RT domain (e.g., a Cas         domain, e.g., a Cas nickase domain, e.g., a Cas9 nickase         domain); optionally wherein the RT domain is C-terminal of the         Cas domain.

In an aspect, the disclosure provides a gene modifying polypeptide comprising:

-   -   a DNA binding domain (DBD) that binds to a target nucleic acid         sequence,     -   the RT domain of an MLVRD RT, or an amino acid sequence having         at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99%         identity thereto, and     -   a linker disposed between the DBD and the RT domain (e.g., a         linker comprising an amino acid sequence as listed in Table 10,         or an amino acid sequence having at least 70%, 75%, 80%, 85%,         90%, 95%, 96%, 97%, 98%, or 99% identity thereto);     -   wherein the DBD is heterologous to the RT domain (e.g., a Cas         domain, e.g., a Cas nickase domain, e.g., a Cas9 nickase         domain); optionally wherein the RT domain is C-terminal of the         Cas domain.

In an aspect, the disclosure provides a gene modifying polypeptide comprising:

-   -   a DNA binding domain (DBD) that binds to a target nucleic acid         sequence,     -   the RT domain of an MMTVB RT, or an amino acid sequence having         at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99%         identity thereto, and     -   a linker disposed between the DBD and the RT domain (e.g., a         linker comprising an amino acid sequence as listed in Table 10,         or an amino acid sequence having at least 70%, 75%, 80%, 85%,         90%, 95%, 96%, 97%, 98%, or 99% identity thereto);     -   wherein the DBD is heterologous to the RT domain (e.g., a Cas         domain, e.g., a Cas nickase domain, e.g., a Cas9 nickase         domain); optionally wherein the RT domain is C-terminal of the         Cas domain.

In an aspect, the disclosure provides a gene modifying polypeptide comprising:

-   -   a DNA binding domain (DBD) that binds to a target nucleic acid         sequence,     -   the RT domain of an MPMV RT, or an amino acid sequence having at         least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99%         identity thereto, and     -   a linker disposed between the DBD and the RT domain (e.g., a         linker comprising an amino acid sequence as listed in Table 10,         or an amino acid sequence having at least 70%, 75%, 80%, 85%,         90%, 95%, 96%, 97%, 98%, or 99% identity thereto);     -   wherein the DBD is heterologous to the RT domain (e.g., a Cas         domain, e.g., a Cas nickase domain, e.g., a Cas9 nickase         domain); optionally wherein the RT domain is C-terminal of the         Cas domain.

In an aspect, the disclosure provides a gene modifying polypeptide comprising:

-   -   a DNA binding domain (DBD) that binds to a target nucleic acid         sequence,     -   the RT domain of an SFVCP RT, or an amino acid sequence having         at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99%         identity thereto, and     -   a linker disposed between the DBD and the RT domain (e.g., a         linker comprising an amino acid sequence as listed in Table 10,         or an amino acid sequence having at least 70%, 75%, 80%, 85%,         90%, 95%, 96%, 97%, 98%, or 99% identity thereto);     -   wherein the DBD is heterologous to the RT domain (e.g., a Cas         domain, e.g., a Cas nickase domain, e.g., a Cas9 nickase         domain); optionally wherein the RT domain is C-terminal of the         Cas domain.

In an aspect, the disclosure provides a gene modifying polypeptide comprising:

-   -   a DNA binding domain (DBD) that binds to a target nucleic acid         sequence,     -   the RT domain of an SMRVH RT, or an amino acid sequence having         at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99%         identity thereto, and     -   a linker disposed between the DBD and the RT domain (e.g., a         linker comprising an amino acid sequence as listed in Table 10,         or an amino acid sequence having at least 70%, 75%, 80%, 85%,         90%, 95%, 96%, 97%, 98%, or 99% identity thereto);     -   wherein the DBD is heterologous to the RT domain (e.g., a Cas         domain, e.g., a Cas nickase domain, e.g., a Cas9 nickase         domain); optionally wherein the RT domain is C-terminal of the         Cas domain.

In an aspect, the disclosure provides a gene modifying polypeptide comprising:

-   -   a DNA binding domain (DBD) that binds to a target nucleic acid         sequence,     -   the RT domain of an SRV1 RT, or an amino acid sequence having at         least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99%         identity thereto, and     -   a linker disposed between the DBD and the RT domain (e.g., a         linker comprising an amino acid sequence as listed in Table 10,         or an amino acid sequence having at least 70%, 75%, 80%, 85%,         90%, 95%, 96%, 97%, 98%, or 99% identity thereto);     -   wherein the DBD is heterologous to the RT domain (e.g., a Cas         domain, e.g., a Cas nickase domain, e.g., a Cas9 nickase         domain); optionally wherein the RT domain is C-terminal of the         Cas domain.

In an aspect, the disclosure provides a gene modifying polypeptide comprising:

-   -   a DNA binding domain (DBD) that binds to a target nucleic acid         sequence,     -   the RT domain of an SRV2 RT, or an amino acid sequence having at         least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99%         identity thereto, and     -   a linker disposed between the DBD and the RT domain (e.g., a         linker comprising an amino acid sequence as listed in Table 10,         or an amino acid sequence having at least 70%, 75%, 80%, 85%,         90%, 95%, 96%, 97%, 98%, or 99% identity thereto);     -   wherein the DBD is heterologous to the RT domain (e.g., a Cas         domain, e.g., a Cas nickase domain, e.g., a Cas9 nickase         domain); optionally wherein the RT domain is C-terminal of the         Cas domain.

In an aspect, the disclosure provides a gene modifying polypeptide comprising:

-   -   a DNA binding domain (DBD) that binds to a target nucleic acid         sequence,     -   the RT domain of an WDSV RT, or an amino acid sequence having at         least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99%         identity thereto, and     -   a linker disposed between the DBD and the RT domain (e.g., a         linker comprising an amino acid sequence as listed in Table 10,         or an amino acid sequence having at least 70%, 75%, 80%, 85%,         90%, 95%, 96%, 97%, 98%, or 99% identity thereto);     -   wherein the DBD is heterologous to the RT domain (e.g., a Cas         domain, e.g., a Cas nickase domain, e.g., a Cas9 nickase         domain); optionally wherein the RT domain is C-terminal of the         Cas domain.

Gene Modifying Domain (RT Domain)

In certain aspects of the present invention, the gene modifying domain of the gene modifying system possesses reverse transcriptase activity and is also referred to as a reverse transcriptase domain (an RT domain). In some embodiments, the RT domain comprises an RT catalytic portion and RNA-binding region (e.g., a region that binds the template RNA).

In some embodiments, a nucleic acid encoding the reverse transcriptase is altered from its natural sequence to have altered codon usage, e.g. improved for human cells. In some embodiments the reverse transcriptase domain is a heterologous reverse transcriptase from a retrovirus. In some embodiments, the RT domain comprising a gene modifying polypeptide has been mutated from its original amino acid sequence, e.g., has at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100 substitutions. In some embodiments, the RT domain is derived from the RT of a retrovirus, e.g., HIV-1 RT, Moloney Murine Leukemia Virus (MMLV) RT, avian myeloblastosis virus (AMV) RT, or Rous Sarcoma Virus (RSV) RT.

In some embodiments, the retroviral reverse transcriptase (RT) domain exhibits enhanced stringency of target-primed reverse transcription (TPRT) initiation, e.g., relative to an endogenous RT domain. In some embodiments, the RT domain initiates TPRT when the 3 nt in the target site immediately upstream of the first strand nick, e.g., the genomic DNA priming the RNA template, have at least 66% or 100% complementarity to the 3 nt of homology in the RNA template. In some embodiments, the RT domain initiates TPRT when there are less than 5 nt mismatched (e.g., less than 1, 2, 3, 4, or 5 nt mismatched) between the template RNA homology and the target DNA priming reverse transcription. In some embodiments, the RT domain is modified such that the stringency for mismatches in priming the TPRT reaction is increased, e.g., wherein the RT domain does not tolerate any mismatches or tolerates fewer mismatches in the priming region relative to a wild-type (e.g., unmodified) RT domain. In some embodiments, the RT domain comprises a HIV-1 RT domain. In embodiments, the HIV-1 RT domain initiates lower levels of synthesis even with three nucleotide mismatches relative to an alternative RT domain (e.g., as described by Jamburuthugoda and Eickbush J Mol Biol 407(5):661-672 (2011); incorporated herein by reference in its entirety). In some embodiments, the RT domain forms a dimer (e.g., a heterodimer or homodimer). In some embodiments, the RT domain is monomeric. In some embodiments, an RT domain, naturally functions as a monomer or as a dimer (e.g., heterodimer or homodimer). In some embodiments, an RT domain naturally functions as a monomer, e.g., is derived from a virus wherein it functions as a monomer. In embodiments, the RT domain is selected from an RT domain from murine leukemia virus (MLV; sometimes referred to as MoMLV) (e.g., P03355), porcine endogenous retrovirus (PERV) (e.g., UniProt Q4VFZ2), mouse mammary tumor virus (MMTV) (e.g., UniProt P03365), Mason-Pfizer monkey virus (MPMV) (e.g., UniProt P07572), bovine leukemia virus (BLV) (e.g., UniProt P03361), human T-cell leukemia virus-1 (HTLV-1) (e.g., UniProt P03362), human foamy virus (HFV) (e.g., UniProt P14350), simian foamy virus (SFV) (e.g., UniProt P23074), or bovine foamy/syncytial virus (BFV/BSV) (e.g., UniProt 041894), or a functional fragment or variant thereof (e.g., an amino acid sequence having at least 70%, 80%, 90%, 95%, or 99% identity thereto). In some embodiments, an RT domain is dimeric in its natural functioning. In some embodiments, the RT domain is derived from a virus wherein it functions as a dimer. In embodiments, the RT domain is selected from an RT domain from avian sarcoma/leukemia virus (ASLV) (e.g., UniProt A0A142BKH1), Rous sarcoma virus (RSV) (e.g., UniProt P03354), avian myeloblastosis virus (AMV) (e.g., UniProt Q83133), human immunodeficiency virus type I (HIV-1) (e.g., UniProt P03369), human immunodeficiency virus type II (HIV-2) (e.g., UniProt P15833), simian immunodeficiency virus (SIV) (e.g., UniProt P05896), bovine immunodeficiency virus (BIV) (e.g., UniProt P19560), equine infectious anemia virus (EIAV) (e.g., UniProt P03371), or feline immunodeficiency virus (FIV) (e.g., UniProt P16088) (Herschhom and Hizi Cell Mol Life Sci 67(16):2717-2747 (2010)), or a functional fragment or variant thereof (e.g., an amino acid sequence having at least 70%, 80%, 90%, 95%, or 99% identity thereto). Naturally heterodimeric RT domains may, in some embodiments, also be functional as homodimers. In some embodiments, dimeric RT domains are expressed as fusion proteins, e.g., as homodimeric fusion proteins or heterodimeric fusion proteins. In some embodiments, the RT function of the system is fulfilled by multiple RT domains (e.g., as described herein). In further embodiments, the multiple RT domains are fused or separate, e.g., may be on the same polypeptide or on different polypeptides.

In some embodiments, a gene modifying system described herein comprises an integrase domain, e.g., wherein the integrase domain may be part of the RT domain. In some embodiments, an RT domain (e.g., as described herein) comprises an integrase domain. In some embodiments, an RT domain (e.g., as described herein) lacks an integrase domain, or comprises an integrase domain that has been inactivated by mutation or deleted. In some embodiment, a gene modifying system described herein comprises an RNase H domain, e.g., wherein the RNase H domain may be part of the RT domain. In some embodiments, the RNase H domain is not part of the RT domain and is covalently linked via a flexible linker. In some embodiments, an RT domain (e.g., as described herein) comprises an RNase H domain, e.g., an endogenous RNAse H domain or a heterologous RNase H domain. In some embodiments, an RT domain (e.g., as described herein) lacks an RNase H domain. In some embodiments, an RT domain (e.g., as described herein) comprises an RNase H domain that has been added, deleted, mutated, or swapped for a heterologous RNase H domain. In some embodiments, the polypeptide comprises an inactivated endogenous RNase H domain. In some embodiments, an endogenous RNase H domain from one of the other domains of the polypeptide is genetically removed such that it is not included in the polypeptide, e.g., the endogenous RNase H domain is partially or completely truncated from the comprising domain. In some embodiments, mutation of an RNase H domain yields a polypeptide exhibiting lower RNase activity, e.g., as determined by the methods described in Kotewicz et al. Nucleic Acids Res 16(1):265-277 (1988) (incorporated herein by reference in its entirety), e.g., lower by at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, or 90% compared to an otherwise similar domain without the mutation. In some embodiments, RNase H activity is abolished.

In some embodiments, an RT domain is mutated to increase fidelity compared to an otherwise similar domain without the mutation. For instance, in some embodiments, a YADD (SEQ ID NO: 15461) or YMDD motif (SEQ ID NO: 15462) in an RT domain (e.g., in a reverse transcriptase) is replaced with YVDD (SEQ ID NO: 15463). In embodiments, replacement of the YADD (SEQ ID NO: 15461) or YMDD (SEQ ID NO: 15462) or YVDD (SEQ ID NO: 15463) results in higher fidelity in retroviral reverse transcriptase activity (e.g., as described in Jamburuthugoda and Eickbush J Mol Biol 2011; incorporated herein by reference in its entirety).

In some embodiments, a gene modifying polypeptide described herein comprises an RT domain having an amino acid sequence according to Table 6, or a sequence having at least 70%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% identity thereto. In some embodiments, a nucleic acid described herein encodes an RT domain having an amino acid sequence according to Table 6, or a sequence having at least 70%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% identity thereto.

TABLE 6 Exemplary reverse transcriptase domains from retroviruses RT Name SEQ ID NO: RT amino acid sequence AVIRE_P03360 8,001 TAPLEEEYRLFLEAPIQNVTLLEQWKREIPKVWAEINPPGLASTQAPIHVQLLSTALPVRVRQYPITLEAKRSLRETIRKFRAAGILRPVHSPWNTPLLPV RKSGTSEYRMVQDLREVNKRVETIHPTVPNPYTLLSLLPPDRIWYSVLDLKDAFFCIPLAPESQLIFAFEWADAEEGESGQLTWTRLPQGFKNSPTLFD EALNRDLQGFRLDHPSVSLLQYVDDLLIAADTQAACLSATRDLLMTLAELGYRVSGKKAQLCQEEVTYLGFKIHKGSRSLSNSRTQAILQIPVPKTKRQV REFLGTIGYCRLWIPGFAELAQPLYAATRGGNDPLVWGEKEEEAFQSLKLALTQPPALALPSLDKPFQLFVEETSGAAKGVLTQALGPWKRPVAYLSK RLDPVAAGWPRCLRAIAAAALLTREASKLTFGQDIEITSSHNLESLLRSPPDKWLTNARITQYQVLLLDPPRVRFKQTAALNPATLLPETDDTLPIHHCLD TLDSLTSTRPDLTDQPLAQAEATLFTDGSSYIRDGKRYAGAAVVTLDSVIWAEPLPIGTSAQKAELIALTKALEWSKDKSVNIYTDSRYAFATLHVHGMIY RERGLLTAGGKAIKNAPEILALLTAVWLPKRVAVMHCKGHQKDDAPTSTGNRRADEVAREVAIRPLSTQATIS AVIRE_P03360_3mut 8,002 TAPLEEEYRLFLEAPIQNVTLLEQWKREIPKVWAEINPPGLASTQAPIHVQLLSTALPVRVRQYPITLEAKRSLRETIRKFRAAGILRPVHSPWNTPLLPV RKSGTSEYRMVQDLREVNKRVETIHPTVPNPYTLLSLLPPDRIWYSVLDLKDAFFCIPLAPESQLIFAFEWADAEEGESGQLTWTRLPQGFKNSPTLFN EALNRDLQGFRLDHPSVSLLQYVDDLLIAADTQAACLSATRDLLMTLAELGYRVSGKKAQLCQEEVTYLGFKIHKGSRSLSNSRTQAILQIPVPKTKRQV REFLGTIGYCRLWIPGFAELAQPLYAATRPGNDPLVWGEKEEEAFQSLKLALTQPPALALPSLDKPFQLFVEETSGAAKGVLTQALGPWKRPVAYLSK RLDPVAAGWPRCLRAIAAAALLTREASKLTFGQDIEITSSHNLESLLRSPPDKWLTNARITQYQVLLLDPPRVRFKQTAALNPATLLPETDDTLPIHHCLD TLDSLTSTRPDLTDQPLAQAEATLFTDGSSYIRDGKRYAGAAVVTLDSVIWAEPLPIGTSAQKAELIALTKALEWSKDKSVNIYTDSRYAFATLHVHGMIY RERGWLTAGGKAIKNAPEILALLTAVWLPKRVAVMHCKGHQKDDAPTSTGNRRADEVAREVAIRPLSTQATIS AVIRE_P03360_3mutA 8,003 TAPLEEEYRLFLEAPIQNVTLLEQWKREIPKVWAEINPPGLASTQAPIHVQLLSTALPVRVRQYPITLEAKRSLRETIRKFRAAGILRPVHSPWNTPLLPV RKSGTSEYRMVQDLREVNKRVETIHPTVPNPYTLLSLLPPDRIWYSVLDLKDAFFCIPLAPESQLIFAFEWADAEEGESGQLTWTRLPQGFKNSPTLFN EALNRDLQGFRLDHPSVSLLQYVDDLLIAADTQAACLSATRDLLMTLAELGYRVSGKKAQLCQEEVTYLGFKIHKGSRSLSNSRTQAILQIPVPKTKRQV REFLGKIGYCRLFIPGFAELAQPLYAATRPGNDPLVWGEKEEEAFQSLKLALTQPPALALPSLDKPFQLFVEETSGAAKGVLTQALGPWKRPVAYLSKR LDPVAAGWPRCLRAIAAAALLTREASKLTFGQDIEITSSHNLESLLRSPPDKWLTNARITQYQVLLLDPPRVRFKQTAALNPATLLPETDDTLPIHHCLDT LDSLTSTRPDLTDQPLAQAEATLFTDGSSYIRDGKRYAGAAVVTLDSVIWAEPLPIGTSAQKAELIALTKALEWSKDKSVNIYTDSRYAFATLHVHGMIY RERGWLTAGGKAIKNAPEILALLTAVWLPKRVAVMHCKGHQKDDAPTSTGNRRADEVAREVAIRPLSTQATIS BAEVM_P10272 8,004 TVSLQDEHRLFDIPVTTSLPDVWLQDFPQAWAETGGLGRAKCQAPIIIDLKPTAVPVSIKQYPMSLEAHMGIRQHIIKFLELGVLRPCRSPWNTPLLPVK KPGTQDYRPVQDLREINKRTVDIHPTVPNPYNLLSTLKPDYSWYTVLDLKDAFFCLPLAPQSQELFAFEWKDPERGISGQLTWTRLPQGFKNSPTLFD EALHRDLTDFRTQHPEVTLLQYVDDLLLAAPTKKACTQGTRHLLQELGEKGYRASAKKAQICQTKVTYLGYILSEGKRWLTPGRIETVARIPPPRNPRE VREFLGTAGFCRLWIPGFAELAAPLYALTKESTPFTWQTEHQLAFEALKKALLSAPALGLPDTSKPFTLFLDERQGIAKGVLTQKLGPWKRPVAYLSKK LDPVAAGWPPCLRIMAATAMLVKDSAKLTLGQPLTVITPHTLEAIVRQPPDRWITNARLTHYQALLLDTDRVQFGPPVTLNPATLLPVPENQPSPHDCR QVLAETHGTREDLKDQELPDADHTWYTDGSSYLDSGTRRAGAAVVDGHNTIWAQSLPPGTSAQKAELIALTKALELSKGKKANIYTDSRYAFATAHTH GSIYERRGLLTSEGKEIKNKAEIIALLKALFLPQEVAIIHCPGHQKGQDPVAVGNRQADRVARQAAMAEVLTLATEPDNTSHIT BAEVM_P10272_3mut 8,005 TVSLQDEHRLFDIPVTTSLPDVWLQDFPQAWAETGGLGRAKCQAPIIIDLKPTAVPVSIKQYPMSLEAHMGIRQHIIKFLELGVLRPCRSPWNTPLLPVK KPGTQDYRPVQDLREINKRTVDIHPTVPNPYNLLSTLKPDYSWYTVLDLKDAFFCLPLAPQSQELFAFEWKDPERGISGQLTWTRLPQGFKNSPTLFN EALHRDLTDFRTQHPEVTLLQYVDDLLLAAPTKKACTQGTRHLLQELGEKGYRASAKKAQICQTKVTYLGYILSEGKRWLTPGRIETVARIPPPRNPRE VREFLGTAGFCRLWIPGFAELAAPLYALTKPSTPFTWQTEHQLAFEALKKALLSAPALGLPDTSKPFTLFLDERQGIAKGVLTQKLGPWKRPVAYLSKK LDPVAAGWPPCLRIMAATAMLVKDSAKLTLGQPLTVITPHTLEAIVRQPPDRWITNARLTHYQALLLDTDRVQFGPPVTLNPATLLPVPENQPSPHDCR QVLAETHGTREDLKDQELPDADHTWYTDGSSYLDSGTRRAGAAVVDGHNTIWAQSLPPGTSAQKAELIALTKALELSKGKKANIYTDSRYAFATAHTH GSIYERRGWLTSEGKEIKNKAEIIALLKALFLPQEVAIIHCPGHQKGQDPVAVGNRQADRVARQAAMAEVLTLATEPDNTSHIT BAEVM_P10272_3mutA 8,006 TVSLQDEHRLFDIPVTTSLPDVWLQDFPQAWAETGGLGRAKCQAPIIIDLKPTAVPVSIKQYPMSLEAHMGIRQHIIKFLELGVLRPCRSPWNTPLLPVK KPGTQDYRPVQDLREINKRTVDIHPTVPNPYNLLSTLKPDYSWYTVLDLKDAFFCLPLAPQSQELFAFEWKDPERGISGQLTWTRLPQGFKNSPTLFN EALHRDLTDFRTQHPEVTLLQYVDDLLLAAPTKKACTQGTRHLLQELGEKGYRASAKKAQICQTKVTYLGYILSEGKRWLTPGRIETVARIPPPRNPRE VREFLGKAGFCRLFIPGFAELAAPLYALTKPSTPFTWQTEHQLAFEALKKALLSAPALGLPDTSKPFTLFLDERQGIAKGVLTQKLGPWKRPVAYLSKKL DPVAAGWPPCLRIMAATAMLVKDSAKLTLGQPLTVITPHTLEAIVRQPPDRWITNARLTHYQALLLDTDRVQFGPPVTLNPATLLPVPENQPSPHDCRQ VLAETHGTREDLKDQELPDADHTWYTDGSSYLDSGTRRAGAAVVDGHNTIWAQSLPPGTSAQKAELIALTKALELSKGKKANIYTDSRYAFATAHTHG SIYERRGWLTSEGKEIKNKAEIIALLKALFLPQEVAIIHCPGHQKGQDPVAVGNRQADRVARQAAMAEVLTLATEPDNTSHIT BLVAU_P25059 8,007 GVLDAPPSHIGLEHLPPPPEVPQFPLNLERLQALQDLVHRSLEAGYISPWDGPGNNPVFPVRKPNGAWRFVHDLRVTNALTKPIPALSPGPPDLTAIPT HLPHIICLDLKDAFFQIPVEDRFRSYFAFTLPTPGGLQPHRRFAWRVLPQGFINSPALFERALQEPLRQVSAAFSQSLLVSYMDDILYVSPTEEQRLQCY QTMAAHLRDLGFQVASEKTRQTPSPVPFLGQMVHERMVTYQSLPTLQISSPISLHQLQTVLGDLQWVSRGTPTTRRPLQLLYSSLKGIDDPRAIIHLSP EQQQGIAELRQALSHNARSRYNEQEPLLAYVHLTRAGSTLVLFQKGAQFPLAYFQTPLTDNQASPWGLLLLLGCQYLQAQALSSYAKTILKYYHNLPK TSLDNWIQSSEDPRVQELLQLWPQISSQGIQPPGPWKTLVTRAEVFLTPQFSPEPIPAALCLFSDGAARRGAYCLWKDHLLDFQAVPAPESAQKGELA GLLAGLAAAPPEPLNIWVDSKYLYSLLRTLVLGAWLQPDPVPSYALLYKSLLRHPAIFVGHVRSHSSASHPIASLNNYVDQL BLVAU_P25059_2mut 8,008 GVLDAPPSHIGLEHLPPPPEVPQFPLNLERLQALQDLVHRSLEAGYISPWDGPGNNPVFPVRKPNGAWRFVHDLRVTNALTKPIPALSPGPPDLTAIPT HLPHIICLDLKDAFFQIPVEDRFRSYFAFTLPTPGGLQPHRRFAWRVLPQGFINSPALFQRALQEPLRQVSAAFSQSLLVSYMDDILYVSPTEEQRLQCY QTMAAHLRDLGFQVASEKTRQTPSPVPFLGQMVHERMVTYQSLPTLQISSPISLHQLQTVLGDLQWVSRGTPTTRRPLQLLYSSLKPIDDPRAIIHLSP EQQQGIAELRQALSHNARSRYNEQEPLLAYVHLTRAGSTLVLFQKGAQFPLAYFQTPLTDNQASPWGLLLLLGCQYLQAQALSSYAKTILKYYHNLPK TSLDNWIQSSEDPRVQELLQLWPQISSQGIQPPGPWKTLVTRAEVFLTPQFSPEPIPAALCLFSDGAARRGAYCLWKDHLLDFQAVPAPESAQKGELA GLLAGLAAAPPEPLNIWVDSKYLYSLLRTLVLGAWLQPDPVPSYALLYKSLLRHPAIFVGHVRSHSSASHPIASLNNYVDQL BLVJ_P03361 8,009 GVLDTPPSHIGLEHLPPPPEVPQFPLNLERLQALQDLVHRSLEAGYISPWDGPGNNPVFPVRKPNGAWRFVHDLRATNALTKPIPALSPGPPDLTAIPT HPPHIICLDLKDAFFQIPVEDRFRFYLSFTLPSPGGLQPHRRFAWRVLPQGFINSPALFERALQEPLRQVSAAFSQSLLVSYMDDILYASPTEEQRSQCY QALAARLRDLGFQVASEKTSQTPSPVPFLGQMVHEQIVTYQSLPTLQISSPISLHQLQAVLGDLQWVSRGTPTTRRPLQLLYSSLKRHHDPRAIIQLSPE QLQGIAELRQALSHNARSRYNEQEPLLAYVHLTRAGSTLVLFQKGAQFPLAYFQTPLTDNQASPWGLLLLLGCQYLQTQALSSYAKPILKYYHNLPKTS LDNWIQSSEDPRVQELLQLWPQISSQGIQPPGPWKTLITRAEVFLTPQFSPDPIPAALCLFSDGATGRGAYCLWKDHLLDFQAVPAPESAQKGELAGL LAGLAAAPPEPVNIWVDSKYLYSLLRTLVLGAWLQPDPVPSYALLYKSLLRHPAIVVGHVRSHSSASHPIASLNNYVDQL BLVJ_P03361_2mut 8,010 GVLDTPPSHIGLEHLPPPPEVPQFPLNLERLQALQDLVHRSLEAGYISPWDGPGNNPVFPVRKPNGAWRFVHDLRATNALTKPIPALSPGPPDLTAIPT HPPHIICLDLKDAFFQIPVEDRFRFYLSFTLPSPGGLQPHRRFAWRVLPQGFINSPALFNRALQEPLRQVSAAFSQSLLVSYMDDILYASPTEEQRSQCY QALAARLRDLGFQVASEKTSQTPSPVPFLGQMVHEQIVTYQSLPTLQISSPISLHQLQAVLGDLQWVSRGTPTTRRPLQLLYSSLKRHHDPRAIIQLSPE QLQGIAELRQALSHNARSRYNEQEPLLAYVHLTRAGSTLVLFQKGAQFPLAYFQTPLTDNQASPWGLLLLLGCQYLQTQALSSYAKPILKYYHNLPKTS LDNWIQSSEDPRVQELLQLWPQISSQGIQPPGPWKTLITRAEVFLTPQFSPDPIPAALCLFSDGATGRGAYCLWKDHLLDFQAVPAPESAQKGELAGL LAGLAAAPPEPVNIWVDSKYLYSLLRTWVLGAWLQPDPVPSYALLYKSLLRHPAIVVGHVRSHSSASHPIASLNNYVDQL BLVJ_P03361_2mutB 8,011 GVLDTPPSHIGLEHLPPPPEVPQFPLNLERLQALQDLVHRSLEAGYISPWDGPGNNPVFPVRKPNGAWRFVHDLRATNALTKPIPALSPGPPDLTAPP THPPHIICLDLKDAFFQIPVEDRFRFYLSFTLPSPGGLQPHRRFAWRVLPQGFINSPALFQRALQEPLRQVSAAFSQSLLVSYMDDILYASPTEEQRSQC YQALAARLRDLGFQVASEKTSQTPSPVPFLGQMVHEQIVTYQSLPTLQISSPISLHQLQAVLGDLQWVSRGTPTTRRPLQLLYSSLKRHHDPRAIIQLSP EQLQGIAELRQALSHNARSRYNEQEPLLAYVHLTRAGSTLVLFQKGAQFPLAYFQTPLTDNQASPWGLLLLLGCQYLQTQALSSYAKPILKYYHNLPKT SLDNWIQSSEDPRVQELLQLWPQISSQGIQPPGPWKTLITRAEVFLTPQFSPDPIPAALCLFSDGATGRGAYCLWKDHLLDFQAVPAPESAQKGELAG LLAGLAAAPPEPVNIWVDSKYLYSLLRTWVLGAWLQPDPVPSYALLYKSLLRHPAIVVGHVRSHSSASHPIASLNNYVDQL FFV_093209 8,012 MDLLKPLTVERKGVKIKGYWNSQADITCVPKDLLQGEEPVRQQNVTTIHGTQEGDVYYVNLKIDGRRINTEVIGTTLDYAIITPGDVPWILKKPLELTIKLD LEEQQGTLLNNSILSKKGKEELKQLFEKYSALWQSWENQVGHRRIRPHKIATGTVKPTPQKQYHINPKAKPDIQIVINDLLKQGVLIQKESTMNTPVYPV PKPNGRWRMVLDYRAVNKVTPLIAVQNQHSYGILGSLFKGRYKTTIDLSNGFWAHPIVPEDYWITAFTWQGKQYCWTVLPQGFLNSPGLFTGDVVDL LQGIPNVEVYVDDVYISHDSEKEHLEYLDILFNRLKEAGYIISLKKSNIANSIVDFLGFQITNEGRGLTDTFKEKLENITAPTTLKQLQSILGLLNFARNFIPDFT ELIAPLYALIPKSTKNYVPWQIEHSTTLETLITKLNGAEYLQGRKGDKTLIMKVNASYTTGYIRYYNEGEKKPISYVSIVFSKTELKFTELEKLLTTVHKG LLKALDLSMGQNIHVYSPIVSMQNIQKTPQTAKKALASRWLSWLSYLEDPRIRFFYDPQMPALKDLPAVDTGKDNKKHPSNFQHIFYTDGSAITSPTKE GHLNAGMGIVYFINKDGNLQKQQEWSISLGNHTAQFAEIAAFEFALKKCLPLGGNILVVTDSNYVAKAYNEELDVWASNGFVNNRKKPLKHISKWKSV ADLKRLRPDVVVTHEPGHQKLDSSPHAYGNNLADQLATQASFKVH FFV_O93209_2mut 8,013 MDLLKPLTVERKGVKIKGYWNSQADITCVPKDLLQGEEPVRQQNVTTIHGTQEGDVYYVNLKIDGRRINTEVIGTTLDYAIITPGDVPWILKKPLELTIKLD LEEQQGTLLNNSILSKKGKEELKQLFEKYSALWQSWENQVGHRRIRPHKIATGTVKPTPQKQYHINPKAKPDIQIVINDLLKQGVLIQKESTMNTPVYPV PKPNGRWRMVLDYRAVNKVTPLIAVQNQHSYGILGSLFKGRYKTTIDLSNGFWAHPIVPEDYWITAFTWQGKQYCWTVLPQGFLNSPGLFNGDVVDL LQGIPNVEVYVDDVYISHDSEKEHLEYLDILFNRLKEAGYIISLKKSNIANSIVDFLGFQITNEGRGLTDTFKEKLENITAPTTLKQLQSILGLLNFARNFIPD FTELIAPLYALIPKSPKNYVPWQIEHSTTLETLITKLNGAEYLQGRKGDKTLIMKVNASYTTGYIRYYNEGEKKPISYVSIVFSKTELKFTELEKLLTTVHKG LLKALDLSMGQNIHVYSPIVSMQNIQKTPQTAKKALASRWLSWLSYLEDPRIRFFYDPQMPALKDLPAVDTGKDNKKHPSNFQHIFYTDGSAITSPTKE GHLNAGMGIVYFINKDGNLQKQQEWSISLGNHTAQFAEIAAFEFALKKCLPLGGNILVVTDSNYVAKAYNEELDVWASNGFVNNRKKPLKHISKWKSV ADLKRLRPDVVVTHEPGHQKLDSSPHAYGNNLADQLATQASFKVH FFV_O93209_2mutA 8,014 MDLLKPLTVERKGVKIKGYWNSQADITCVPKDLLQGEEPVRQQNVTTIHGTQEGDVYYVNLKIDGRRINTEVIGTTLDYAIITPGDVPWILKKPLELTIKLD LEEQQGTLLNNSILSKKGKEELKQLFEKYSALWQSWENQVGHRRIRPHKIATGTVKPTPQKQYHINPKAKPDIQIVINDLLKQGVLIQKESTMNTPVYPV PKPNGRWRMVLDYRAVNKVTPLIAVQNQHSYGILGSLFKGRYKTTIDLSNGFWAHPIVPEDYWITAFTWQGKQYCWTVLPQGFLNSPGLFNGDVVDL LQGIPNVEVYVDDVYISHDSEKEHLEYLDILFNRLKEAGYIISLKKSNIANSIVDFLGFQITNEGRGLTDTFKEKLENITAPTTLKQLQSILGKLNFARNFIPDFTE LIAPLYALIPKSPKNYVPWQIEHSTTLETLITKLNGAEYLQGRKGDKTLIMKVNASYTTGYIRYYNEGEKKPISYVSIVFSKTELKFTELEKLLTTVHKG LLKALDLSMGQNIHVYSPIVSMQNIQKTPQTAKKALASRWLSWLSYLEDPRIRFFYDPQMPALKDLPAVDTGKDNKKHPSNFQHIFYTDGSAITSPTKE GHLNAGMGIVYFINKDGNLQKQQEWSISLGNHTAQFAEIAAFEFALKKCLPLGGNILVVTDSNYVAKAYNEELDVWASNGFVNNRKKPLKHISKWKSV ADLKRLRPDVVVTHEPGHQKLDSSPHAYGNNLADQLATQASFKVH FFV_O93209-Pro 8,015 VPWILKKPLELTIKLDLEEQQGTLLNNSILSKKGKEELKQLFEKYSALWQSWENQVGHRRIRPHKIATGTVKPTPQKQYHINPKAKPDIQIVINDLLKQGV LIQKESTMNTPVYPVPKPNGRWRMVLDYRAVNKVTPLIAVQNQHSYGILGSLFKGRYKTTIDLSNGFWAHPIVPEDYWITAFTWQGKQYCWTVLPQGF LNSPGLFTGDVVDLLQGIPNVEVYVDDVYISHDSEKEHLEYLDILFNRLKEAGYIISLKKSNIANSIVDFLGFQITNEGRGLTDTFKEKLENITAPTTLKQLQ SILGLLNFARNFIPDFTELIAPLYALIPKSTKNYVPWQIEHSTTLETLITKLNGAEYLQGRKGDKTLIMKVNASYTTGYIRYYNEGEKKPISYVSIVFSKTELK FTELEKLLTTVHKGLLKALDLSMGQNIHVYSPIVSMQNIQKTPQTAKKALASRWLSWLSYLEDPRIRFFYDPQMPALKDLPAVDTGKDNKKHPSNFQHI FYTDGSAITSPTKEGHLNAGMGIVYFINKDGNLQKQQEWSISLGNHTAQFAEIAAFEFALKKCLPLGGNILVVTDSNYVAKAYNEELDVWASNGFVNNR KKPLKHISKWKSVADLKRLRPDVVVTHEPGHQKLDSSPHAYGNNLADQLATQASFKVH FFV_O93209-Pro_2mut 8,016 VPWILKKPLELTIKLDLEEQQGTLLNNSILSKKGKEELKQLFEKYSALWQSWENQVGHRRIRPHKIATGTVKPTPQKQYHINPKAKPDIQIVINDLLKQGV LIQKESTMNTPVYPVPKPNGRWRMVLDYRAVNKVTPLIAVQNQHSYGILGSLFKGRYKTTIDLSNGFWAHPIVPEDYWITAFTWQGKQYCWTVLPQGF LNSPGLFNGDVVDLLQGIPNVEVYVDDVYISHDSEKEHLEYLDILFNRLKEAGYIISLKKSNIANSIVDFLGFQITNEGRGLTDTFKEKLENITAPTTLKQLQ SILGLLNFARNFIPDFTELIAPLYALIPKSPKNYVPWQIEHSTTLETLITKLNGAEYLQGRKGDKTLIMKVNASYTTGYIRYYNEGEKKPISYVSIVFSKTELK FTELEKLLTTVHKGLLKALDLSMGQNIHVYSPIVSMQNIQKTPQTAKKALASRWLSWLSYLEDPRIRFFYDPQMPALKDLPAVDTGKDNKKHPSNFQHI FYTDGSAITSPTKEGHLNAGMGIVYFINKDGNLQKQQEWSISLGNHTAQFAEIAAFEFALKKCLPLGGNILVVTDSNYVAKAYNEELDVWASNGFVNNR KKPLKHISKWKSVADLKRLRPDVVVTHEPGHQKLDSSPHAYGNNLADQLATQASFKVH FFV_O93209-Pro_2mutA 8,017 VPWILKKPLELTIKLDLEEQQGTLLNNSILSKKGKEELKQLFEKYSALWQSWENQVGHRRIRPHKIATGTVKPTPQKQYHINPKAKPDIQIVINDLLKQGV LIQKESTMNTPVYPVPKPNGRWRMVLDYRAVNKVTPLIAVQNQHSYGILGSLFKGRYKTTIDLSNGFWAHPIVPEDYWITAFTWQGKQYCWTVLPQGF LNSPGLFNGDVVDLLQGIPNVEVYVDDVYISHDSEKEHLEYLDILFNRLKEAGYIISLKKSNIANSIVDFLGFQITNEGRGLTDTFKEKLENITAPTTLKQLQ SILGKLNFARNFIPDFTELIAPLYALIPKSPKNYVPWQIEHSTTLETLITKLNGAEYLQGRKGDKTLIMKVNASYTTGYIRYYNEGEKKPISYVSIVFSKTELK FTELEKLLTTVHKGLLKALDLSMGQNIHVYSPIVSMQNIQKTPQTAKKALASRWLSWLSYLEDPRIRFFYDPQMPALKDLPAVDTGKDNKKHPSNFQHI FYTDGSAITSPTKEGHLNAGMGIVYFINKDGNLQKQQEWSISLGNHTAQFAEIAAFEFALKKCLPLGGNILVVTDSNYVAKAYNEELDVWASNGFVNNR KKPLKHISKWKSVADLKRLRPDVVVTHEPGHQKLDSSPHAYGNNLADQLATQASFKVH FLV_P10273 8,018 TLQLEEEYRLFEPESTQKQEMDIWLKNFPQAWAETGGMGTAHCQAPVLIQLKATATPISIRQYPMPHEAYQGIKPHIRRMLDQGILKPCQSPWNTPLLP VKKPGTEDYRPVQDLREVNKRVEDIHPTVPNPYNLLSTLPPSHPWYTVLDLKDAFFCLRLHSESQLLFAFEWRDPEIGLSGQLTWTRLPQGFKNSPTL FDEALHSDLADFRVRYPALVLLQYVDDLLLAAATRTECLEGTKALLETLGNKGYRASAKKAQICLQEVTYLGYSLKDGQRWLTKARKEAILSIPVPKNSR QVREFLGTAGYCRLWIPGFAELAAPLYPLTRPGTLFQWGTEQQLAFEDIKKALLSSPALGLPDITKPFELFIDENSGFAKGVLVQKLGPWKRPVAYLSK KLDTVASGWPPCLRMVAAIAILVKDAGKLTLGQPLTILTSHPVEALVRQPPNKWLSNARMTHYQAMLLDAERVHFGPTVSLNPATLLPLPSGGNHHDC LQILAETHGTRPDLTDQPLPDADLTWYTDGSSFIRNGEREAGAAVTTESEVIWAAPLPPGTSAQRAELIALTQALKMAEGKKLTVYTDSRYAFATTHVH GEIYRRRGLLTSEGKEIKNKNEILALLEALFLPKRLSIIHCPGHQKGDSPQAKGNRLADDTAKKAATETHSSLTVLP FLV_P10273_3mut 8,019 TLQLEEEYRLFEPESTQKQEMDIWLKNFPQAWAETGGMGTAHCQAPVLIQLKATATPISIRQYPMPHEAYQGIKPHIRRMLDQGILKPCQSPWNTPLLP VKKPGTEDYRPVQDLREVNKRVEDIHPTVPNPYNLLSTLPPSHPWYTVLDLKDAFFCLRLHSESQLLFAFEWRDPEIGLSGQLTWTRLPQGFKNSPTL FNEALHSDLADFRVRYPALVLLQYVDDLLLAAATRTECLEGTKALLETLGNKGYRASAKKAQICLQEVTYLGYSLKDGQRWLTKARKEAILSIPVPKNSR QVREFLGTAGYCRLWIPGFAELAAPLYPLTRPGTLFQWGTEQQLAFEDIKKALLSSPALGLPDITKPFELFIDENSGFAKGVLVQKLGPWKRPVAYLSK KLDTVASGWPPCLRMVAAIAILVKDAGKLTLGQPLTILTSHPVEALVRQPPNKWLSNARMTHYQAMLLDAERVHFGPTVSLNPATLLPLPSGGNHHDC LQILAETHGTRPDLTDQPLPDADLTWYTDGSSFIRNGEREAGAAVTTESEVIWAAPLPPGTSAQRAELIALTQALKMAEGKKLTVYTDSRYAFATTHVH GEIYRRRGWLTSEGKEIKNKNEILALLEALFLPKRLSIIHCPGHQKGDSPQAKGNRLADDTAKKAATETHSSLTVLP FLV_P10273_3mutA 8,020 TLQLEEEYRLFEPESTQKQEMDIWLKNFPQAWAETGGMGTAHCQAPVLIQLKATATPISIRQYPMPHEAYQGIKPHIRRMLDQGILKPCQSPWNTPLLP VKKPGTEDYRPVQDLREVNKRVEDIHPTVPNPYNLLSTLPPSHPWYTVLDLKDAFFCLRLHSESQLLFAFEWRDPEIGLSGQLTWTRLPQGFKNSPTL FNEALHSDLADFRVRYPALVLLQYVDDLLLAAATRTECLEGTKALLETLGNKGYRASAKKAQICLQEVTYLGYSLKDGQRWLTKARKEAILSIPVPKNSR QVREFLGKAGYCRLFIPGFAELAAPLYPLTRPGTLFQWGTEQQLAFEDIKKALLSSPALGLPDITKPFELFIDENSGFAKGVLVQKLGPWKRPVAYLSKK LDTVASGWPPCLRMVAAIAILVKDAGKLTLGQPLTILTSHPVEALVRQPPNKWLSNARMTHYQAMLLDAERVHFGPTVSLNPATLLPLPSGGNHHDCL QILAETHGTRPDLTDQPLPDADLTWYTDGSSFIRNGEREAGAAVTTESEVIWAAPLPPGTSAQRAELIALTQALKMAEGKKLTVYTDSRYAFATTHVHG EIYRRRGWLTSEGKEIKNKNEILALLEALFLPKRLSIIHCPGHQKGDSPQAKGNRLADDTAKKAATETHSSLTVLP FOAMV_P14350 8,021 MNPLQLLQPLPAEIKGTKLLAHWNSGATITCIPESFLEDEQPIKKTLIKTIHGEKQQNVYYVTFKVKGRKVEAEVIASPYEYILLSPTDVPWLTQQPLQLTIL VPLQEYQEKILSKTALPEDQKQQLKTLFVKYDNLWQHWENQVGHRKIRPHNIATGDYPPRPQKQYPINPKAKPSIQIVIDDLLKQGVLTPQNSTMNTPV YPVPKPDGRWRMVLDYREVNKTIPLTAAQNQHSAGILATIVRQKYKTTLDLANGFWAHPITPESYWLTAFTWQGKQYCWTRLPQGFLNSPALFTADV VDLLKEIPNVQVYVDDIYLSHDDPKEHVQQLEKVFQILLQAGYVVSLKKSEIGQKTVEFLGFNITKEGRGLTDTFKTKLLNITPPKDLKQLQSILGLLNFAR NFIPNFAELVQPLYNLIASAKGKYIEWSEENTKQLNMVIEALNTASNLEERLPEQRLVIKVNTSPSAGYVRYYNETGKKPIMYLNYVFSKAELKFSMLEKL LTTMHKALIKAMDLAMGQEILVYSPIVSMTKIQKTPLPERKALPIRWITWMTYLEDPRIQFHYDKTLPELKHIPDVYTSSQSPVKHPSQYEGVFYTDGSAI KSPDPTKSNNAGMGIVHATYKPEYQVLNQWSIPLGNHTAQMAEIAAVEFACKKALKIPGPVLVITDSFYVAESANKELPYWKSNGFVNNKKKPLKHISK WKSIAECLSMKPDITIQHEKGISLQIPVFILKGNALADKLATQGSYVVN FOAMV_P14350_2mut 8,022 MNPLQLLQPLPAEIKGTKLLAHWNSGATITCIPESFLEDEQPIKKTLIKTIHGEKQQNVYYVTFKVKGRKVEAEVIASPYEYILLSPTDVPWLTQQPLQLTIL VPLQEYQEKILSKTALPEDQKQQLKTLFVKYDNLWQHWENQVGHRKIRPHNIATGDYPPRPQKQYPINPKAKPSIQIVIDDLLKQGVLTPQNSTMNTPV YPVPKPDGRWRMVLDYREVNKTIPLTAAQNQHSAGILATIVRQKYKTTLDLANGFWAHPITPESYWLTAFTWQGKQYCWTRLPQGFLNSPALFNADV VDLLKEIPNVQVYVDDIYLSHDDPKEHVQQLEKVFQILLQAGYVVSLKKSEIGQKTVEFLGFNITKEGRGLTDTFKTKLLNITPPKDLKQLQSILGLLNFAR NFIPNFAELVQPLYNLIAPAKGKYIEWSEENTKQLNMVIEALNTASNLEERLPEQRLVIKVNTSPSAGYVRYYNETGKKPIMYLNYVFSKAELKFSMLEKL LTTMHKALIKAMDLAMGQEILVYSPIVSMTKIQKTPLPERKALPIRWITWMTYLEDPRIQFHYDKTLPELKHIPDVYTSSQSPVKHPSQYEGVFYTDGSAI KSPDPTKSNNAGMGIVHATYKPEYQVLNQWSIPLGNHTAQMAEIAAVEFACKKALKIPGPVLVITDSFYVAESANKELPYWKSNGFVNNKKKPLKHISK WKSIAECLSMKPDITIQHEKGISLQIPVFILKGNALADKLATQGSYVVN FOAMV_P14350_2mutA 8,023 MNPLQLLQPLPAEIKGTKLLAHWNSGATITCIPESFLEDEQPIKKTLIKTIHGEKQQNVYYVTFKVKGRKVEAEVIASPYEYILLSPTDVPWLTQQPLQLTIL VPLQEYQEKILSKTALPEDQKQQLKTLFVKYDNLWQHWENQVGHRKIRPHNIATGDYPPRPQKQYPINPKAKPSIQIVIDDLLKQGVLTPQNSTMNTPV YPVPKPDGRWRMVLDYREVNKTIPLTAAQNQHSAGILATIVRQKYKTTLDLANGFWAHPITPESYWLTAFTWQGKQYCWTRLPQGFLNSPALFNADV VDLLKEIPNVQVYVDDIYLSHDDPKEHVQQLEKVFQILLQAGYVVSLKKSEIGQKTVEFLGFNITKEGRGLTDTFKTKLLNITPPKDLKQLQSILGKLNFAR NFIPNFAELVQPLYNLIAPAKGKYIEWSEENTKQLNMVIEALNTASNLEERLPEQRLVIKVNTSPSAGYVRYYNETGKKPIMYLNYVFSKAELKFSMLEKL LTTMHKALIKAMDLAMGQEILVYSPIVSMTKIQKTPLPERKALPIRWITWMTYLEDPRIQFHYDKTLPELKHIPDVYTSSQSPVKHPSQYEGVFYTDGSAI KSPDPTKSNNAGMGIVHATYKPEYQVLNQWSIPLGNHTAQMAEIAAVEFACKKALKIPGPVLVITDSFYVAESANKELPYWKSNGFVNNKKKPLKHISK WKSIAECLSMKPDITIQHEKGISLQIPVFILKGNALADKLATQGSYVVN FOAMV_P14350-Pro 8,024 VPWLTQQPLQLTILVPLQEYQEKILSKTALPEDQKQQLKTLFVKYDNLWQHWENQVGHRKIRPHNIATGDYPPRPQKQYPINPKAKPSIQIVIDDLLKQG VLTPQNSTMNTPVYPVPKPDGRWRMVLDYREVNKTIPLTAAQNQHSAGILATIVRQKYKTTLDLANGFWAHPITPESYWLTAFTWQGKQYCWTRLPQ GFLNSPALFTADVVDLLKEIPNVQVYVDDIYLSHDDPKEHVQQLEKVFQILLQAGYVVSLKKSEIGQKTVEFLGFNITKEGRGLTDTFKTKLLNITPPKDLK QLQSILGLLNFARNFIPNFAELVQPLYNLIASAKGKYIEWSEENTKQLNMVIEALNTASNLEERLPEQRLVIKVNTSPSAGYVRYYNETGKKPIMYLNYVF SKAELKFSMLEKLLTTMHKALIKAMDLAMGQEILVYSPIVSMTKIQKTPLPERKALPIRWITWMTYLEDPRIQFHYDKTLPELKHIPDVYTSSQSPVKHPS QYEGVFYTDGSAIKSPDPTKSNNAGMGIVHATYKPEYQVLNQWSIPLGNHTAQMAEIAAVEFACKKALKIPGPVLVITDSFYVAESANKELPYWKSNGF VNNKKKPLKHISKWKSIAECLSMKPDITIQHEKGISLQIPVFILKGNALADKLATQGSYVVN FOAMV_P14350-Pro_2mut 8,025 VPWLTQQPLQLTILVPLQEYQEKILSKTALPEDQKQQLKTLFVKYDNLWQHWENQVGHRKIRPHNIATGDYPPRPQKQYPINPKAKPSIQIVIDDLLKQG VLTPQNSTMNTPVYPVPKPDGRWRMVLDYREVNKTIPLTAAQNQHSAGILATIVRQKYKTTLDLANGFWAHPITPESYWLTAFTWQGKQYCWTRLPQ GFLNSPALFNADVVDLLKEIPNVQVYVDDIYLSHDDPKEHVQQLEKVFQILLQAGYVVSLKKSEIGQKTVEFLGFNITKEGRGLTDTFKTKLLNITPPKDL KQLQSILGLLNFARNFIPNFAELVQPLYNLIAPAKGKYIEWSEENTKQLNMVIEALNTASNLEERLPEQRLVIKVNTSPSAGYVRYYNETGKKPIMYLNYV FSKAELKFSMLEKLLTTMHKALIKAMDLAMGQEILVYSPIVSMTKIQKTPLPERKALPIRWITWMTYLEDPRIQFHYDKTLPELKHIPDVYTSSQSPVKHP SQYEGVFYTDGSAIKSPDPTKSNNAGMGIVHATYKPEYQVLNQWSIPLGNHTAQMAEIAAVEFACKKALKIPGPVLVITDSFYVAESANKELPYWKSNG FVNNKKKPLKHISKWKSIAECLSMKPDITIQHEKGISLQIPVFILKGNALADKLATQGSYVVN FOAMV_P14350-Pro_2mutA 8,026 VPWLTQQPLQLTILVPLQEYQEKILSKTALPEDQKQQLKTLFVKYDNLWQHWENQVGHRKIRPHNIATGDYPPRPQKQYPINPKAKPSIQIVIDDLLKQG VLTPQNSTMNTPVYPVPKPDGRWRMVLDYREVNKTIPLTAAQNQHSAGILATIVRQKYKTTLDLANGFWAHPITPESYWLTAFTWQGKQYCWTRLPQ GFLNSPALFNADVVDLLKEIPNVQVYVDDIYLSHDDPKEHVQQLEKVFQILLQAGYVVSLKKSEIGQKTVEFLGFNITKEGRGLTDTFKTKLLNITPPKDL KQLQSILGKLNFARNFIPNFAELVQPLYNLIAPAKGKYIEWSEENTKQLNMVIEALNTASNLEERLPEQRLVIKVNTSPSAGYVRYYNETGKKPIMYLNYV FSKAELKFSMLEKLLTTMHKALIKAMDLAMGQEILVYSPIVSMTKIQKTPLPERKALPIRWITWMTYLEDPRIQFHYDKTLPELKHIPDVYTSSQSPVKHP SQYEGVFYTDGSAIKSPDPTKSNNAGMGIVHATYKPEYQVLNQWSIPLGNHTAQMAEIAAVEFACKKALKIPGPVLVITDSFYVAESANKELPYWKSNG FVNNKKKPLKHISKWKSIAECLSMKPDITIQHEKGISLQIPVFILKGNALADKLATQGSYVVN GALV_P21414 8,027 VLNLEEEYRLHEKPVPSSIDPSWLQLFPTVWAERAGMGLANQVPPVVVELRSGASPVAVRQYPMSKEAREGIRPHIQKFLDLGVLVPCRSPWNTPLL PVKKPGTNDYRPVQDLREINKRVQDIHPTVPNPYNLLSSLPPSYTWYSVLDLKDAFFCLRLHPNSQPLFAFEWKDPEKGNTGQLTWTRLPQGFKNSP TLFDEALHRDLAPFRALNPQVVLLQYVDDLLVAAPTYEDCKKGTQKLLQELSKLGYRVSAKKAQLCQREVTYLGYLLKEGKRWLTPARKATVMKIPVP TTPRQVREFLGTAGFCRLWIPGFASLAAPLYPLTKESIPFIWTEEHQQAFDHIKKALLSAPALALPDLTKPFTLYIDERAGVARGVLTQTLGPWRRPVAY LSKKLDPVASGWPTCLKAVAAVALLLKDADKLTLGQNVTVIASHSLESIVRQPPDRWMTNARMTHYQSLLLNERVSFAPPAVLNPATLLPVESEATPVH RCSEILAEETGTRRDLEDQPLPGVPTWYTDGSSFITEGKRRAGAPIVDGKRTVWASSLPEGTSAQKAELVALTQALRLAEGKNINIYTDSRYAFATAHIH GAIYKQRGLLTSAGKDIKNKEEILALLEAIHLPRRVAIIHCPGHQRGSNPVATGNRRADEAAKQAALSTRVLAGTTKP GALV_P21414_3mut 8,028 VLNLEEEYRLHEKPVPSSIDPSWLQLFPTVWAERAGMGLANQVPPVVVELRSGASPVAVRQYPMSKEAREGIRPHIQKFLDLGVLVPCRSPWNTPLL PVKKPGTNDYRPVQDLREINKRVQDIHPTVPNPYNLLSSLPPSYTWYSVLDLKDAFFCLRLHPNSQPLFAFEWKDPEKGNTGQLTWTRLPQGFKNSP TLFNEALHRDLAPFRALNPQVVLLQYVDDLLVAAPTYEDCKKGTQKLLQELSKLGYRVSAKKAQLCQREVTYLGYLLKEGKRWLTPARKATVMKIPVP TTPRQVREFLGTAGFCRLWIPGFASLAAPLYPLTKPSIPFIWTEEHQQAFDHIKKALLSAPALALPDLTKPFTLYIDERAGVARGVLTQTLGPWRRPVAY LSKKLDPVASGWPTCLKAVAAVALLLKDADKLTLGQNVTVIASHSLESIVRQPPDRWMTNARMTHYQSLLLNERVSFAPPAVLNPATLLPVESEATPVH RCSEILAEETGTRRDLEDQPLPGVPTWYTDGSSFITEGKRRAGAPIVDGKRTVWASSLPEGTSAQKAELVALTQALRLAEGKNINIYTDSRYAFATAHIH GAIYKQRGWLTSAGKDIKNKEEILALLEAIHLPRRVAIIHCPGHQRGSNPVATGNRRADEAAKQAALSTRVLAGTTKP GALV_P21414_3mutA 8,029 VLNLEEEYRLHEKPVPSSIDPSWLQLFPTVWAERAGMGLANQVPPVVVELRSGASPVAVRQYPMSKEAREGIRPHIQKFLDLGVLVPCRSPWNTPLL PVKKPGTNDYRPVQDLREINKRVQDIHPTVPNPYNLLSSLPPSYTWYSVLDLKDAFFCLRLHPNSQPLFAFEWKDPEKGNTGQLTWTRLPQGFKNSP TLFNEALHRDLAPFRALNPQVVLLQYVDDLLVAAPTYEDCKKGTQKLLQELSKLGYRVSAKKAQLCQREVTYLGYLLKEGKRWLTPARKATVMKIPVP TTPRQVREFLGKAGFCRLFIPGFASLAAPLYPLTKPSIPFIWTEEHQQAFDHIKKALLSAPALALPDLTKPFTLYIDERAGVARGVLTQTLGPWRRPVAYL SKKLDPVASGWPTCLKAVAAVALLLKDADKLTLGQNVTVIASHSLESIVRQPPDRWMTNARMTHYQSLLLNERVSFAPPAVLNPATLLPVESEATPVH RCSEILAEETGTRRDLEDQPLPGVPTWYTDGSSFITEGKRRAGAPIVDGKRTVWASSLPEGTSAQKAELVALTQALRLAEGKNINIYTDSRYAFATAHIH GAIYKQRGWLTSAGKDIKNKEEILALLEAIHLPRRVAIIHCPGHQRGSNPVATGNRRADEAAKQAALSTRVLAGTTKP HTL1A_P03362 8,030 AVLGLEHLPRPPQISQFPLNPERLQALQHLVRKALEAGHIEPYTGPGNNPVFPVKKANGTWRFIHDLRATNSLTIDLSSSSPGPPDLSSLPTTLAHLQTI DLRDAFFQIPLPKQFQPYFAFTVPQQCNYGPGTRYAWKVLPQGFKNSPTLFEMQLAHILQPIRQAFPQCTILQYMDDILLASPSHEDLLLLSEATMASLI SHGLPVSENKTQQTPGTIKFLGQIISPNHLTYDAVPTVPIRSRWALPELQALLGEIQWVSKGTPTLRQPLHSLYCALQRHTDPRDQIYLNPSQVQSLVQL RQALSQNCRSRLVQTLPLLGAIMLTLTGTTTVVFQSKEQWPLVWLHAPLPHTSQCPWGQLLASAVLLLDKYTLQSYGLLCQTIHHNISTQTFNQFIQTS DHPSVPILLHHSHRFKNLGAQTGELWNTFLKTAAPLAPVKALMPVFTLSPVIINTAPCLFSDGSTSRAAYILWDKQILSQRSFPLPPPHKSAQRAELLGLL HGLSSARSWRCLNIFLDSKYLYHYLRTLALGTFQGRSSQAPFQALLPRLLSRKVVYLHHVRSHTNLPDPISRLNALTDALLITPVLQL HTL1A_P03362_2mut 8,031 AVLGLEHLPRPPQISQFPLNPERLQALQHLVRKALEAGHIEPYTGPGNNPVFPVKKANGTWRFIHDLRATNSLTIDLSSSSPGPPDLSSLPTTLAHLQTI DLRDAFFQIPLPKQFQPYFAFTVPQQCNYGPGTRYAWKVLPQGFKNSPTLFQMQLAHILQPIRQAFPQCTILQYMDDILLASPSHEDLLLLSEATMASLI SHGLPVSENKTQQTPGTIKFLGQIISPNHLTYDAVPTVPIRSRWALPELQALLGEIQWVSKGTPTLRQPLHSLYCALQPHTDPRDQIYLNPSQVQSLVQL RQALSQNCRSRLVQTLPLLGAIMLTLTGTTTVVFQSKEQWPLVWLHAPLPHTSQCPWGQLLASAVLLLDKYTLQSYGLLCQTIHHNISTQTFNQFIQTS DHPSVPILLHHSHRFKNLGAQTGELWNTFLKTAAPLAPVKALMPVFTLSPVIINTAPCLFSDGSTSRAAYILWDKQILSQRSFPLPPPHKSAQRAELLGLL HGLSSARSWRCLNIFLDSKYLYHYLRTLALGTFQGRSSQAPFQALLPRLLSRKVVYLHHVRSHTNLPDPISRLNALTDALLITPVLQL HTL1A_P03362_2mutB 8,032 AVLGLEHLPRPPQISQFPLNPERLQALQHLVRKALEAGHIEPYTGPGNNPVFPVKKANGTWRFIHDLRATNSLTIDLSSSSPGPPDLSSPPTTLAHLQTI DLRDAFFQIPLPKQFQPYFAFTVPQQCNYGPGTRYAWKVLPQGFKNSPTLFQMQLAHILQPIRQAFPQCTILQYMDDILLASPSHEDLLLLSEATMASLI SHGLPVSENKTQQTPGTIKFLGQIISPNHLTYDAVPTVPIRSRWALPELQALLGEIQWVSKGTPTLRQPLHSLYCALQPHTDPRDQIYLNPSQVQSLVQL RQALSQNCRSRLVQTLPLLGAIMLTLTGTTTVVFQSKEQWPLVWLHAPLPHTSQCPWGQLLASAVLLLDKYTLQSYGLLCQTIHHNISTQTFNQFIQTS DHPSVPILLHHSHRFKNLGAQTGELWNTFLKTAAPLAPVKALMPVFTLSPVIINTAPCLFSDGSTSRAAYILWDKQILSQRSFPLPPPHKSAQRAELLGLL HGLSSARSWRCLNIFLDSKYLYHYLRTLALGTFQGRSSQAPFQALLPRLLSRKVVYLHHVRSHTNLPDPISRLNALTDALLITPVLQL HTL1C_P14078 8,033 AVLGLEHLPRPPEISQFPLNPERLQALQHLVRKALEAGHIEPYTGPGNNPVFPVKKANGTWRFIHDLRATNSLTIDLSSSSPGPPDLSSLPTTLAHLQTI DLKDAFFQIPLPKQFQPYFAFTVPQQCNYGPGTRYAWRVLPQGFKNSPTLFEMQLAHILQPIRQAFPQCTILQYMDDILLASPSHADLQLLSEATMASLI SHGLPVSENKTQQTPGTIKFLGQIISPNHLTYDAVPKVPIRSRWALPELQALLGEIQWVSKGTPTLRQPLHSLYCALQRHTDPRDQIYLNPSQVQSLVQL RQALSQNCRSRLVQTLPLLGAIMLTLTGTTTVVFQSKQQWPLVWLHAPLPHTSQCPWGQLLASAVLLLDKYTLQSYGLLCQTIHHNISTQTFNQFIQTS DHPSVPILLHHSHRFKNLGAQTGELWNTFLKTTAPLAPVKALMPVFTLSPVIINTAPCLFSDGSTSQAAYILWDKHILSQRSFPLPPPHKSAQRAELLGLL HGLSSARSWRCLNIFLDSKYLYHYLRTLALGTFQGRSSQAPFQALLPRLLSRKVVYLHHVRSHTNLPDPISRLNALTDALLITPVLQL HTL1C_P14078_2mut 8,034 AVLGLEHLPRPPEISQFPLNPERLQALQHLVRKALEAGHIEPYTGPGNNPVFPVKKANGTWRFIHDLRATNSLTIDLSSSSPGPPDLSSLPTTLAHLQTI DLKDAFFQIPLPKQFQPYFAFTVPQQCNYGPGTRYAWRVLPQGFKNSPTLFQMQLAHILQPIRQAFPQCTILQYMDDILLASPSHADLQLLSEATMASLI SHGLPVSENKTQQTPGTIKFLGQIISPNHLTYDAVPKVPIRSRWALPELQALLGEIQWVSKGTPTLRQPLHSLYCALQPHTDPRDQIYLNPSQVQSLVQL RQALSQNCRSRLVQTLPLLGAIMLTLTGTTTVVFQSKQQWPLVWLHAPLPHTSQCPWGQLLASAVLLLDKYTLQSYGLLCQTIHHNISTQTFNQFIQTS DHPSVPILLHHSHRFKNLGAQTGELWNTFLKTTAPLAPVKALMPVFTLSPVIINTAPCLFSDGSTSQAAYILWDKHILSQRSFPLPPPHKSAQRAELLGLL HGLSSARSWRCLNIFLDSKYLYHYLRTLALGTFQGRSSQAPFQALLPRLLSRKVVYLHHVRSHTNLPDPISRLNALTDALLITPVLQL HTL1L_P0C211 8,035 GLEHLPRPPEISQFPLNPERLQALQHLVRKALEAGHIEPYTGPGNNPVFPVKKANGTWRFIHDLRATNSLTVDLSSSSPGPPDLSSLPTTLAHLQTIDLK DAFFQIPLPKQFQPYFAFTVPQQCNYGPGTRYAWKVLPQGFKNSPTLFEMQLASILQPIRQAFPQCVILQYMDDILLASPSPEDLQQLSEATMASLISH GLPVSQDKTQQTPGTIKFLGQIISPNHITYDAVPTVPIRSRWALPELQALLGEIQWVSKGTPTLRQPLHSLYCALQGHTDPRDQIYLNPSQVQSLMQLQ QALSQNCRSRLAQTLPLLGAIMLTLTGTTTVVFQSKQQWPLVWLHAPLPHTSQCPWGQLLASAVLLLDKYTLQSYGLLCQTIHHNISIQTFNQFIQTSD HPSVPILLHHSHRFKNLGAQTGELWNTFLKTAAPLAPVKALTPVFTLSPIIINTAPCLFSDGSTSQAAYILWDKHILSQRSFPLPPPHKSAQQAELLGLLH GLSSARSWHCLNIFLDSKYLYHYLRTLALGTFQGKSSQAPFQALLPRLLAHKVIYLHHVRSHTNLPDPISKLNALTDALLITPIL HTL1L_P0C211_2mut 8,036 GLEHLPRPPEISQFPLNPERLQALQHLVRKALEAGHIEPYTGPGNNPVFPVKKANGTWRFIHDLRATNSLTVDLSSSSPGPPDLSSLPTTLAHLQTIDLK DAFFQIPLPKQFQPYFAFTVPQQCNYGPGTRYAWKVLPQGFKNSPTLFQMQLASILQPIRQAFPQCVILQYMDDILLASPSPEDLQQLSEATMASLISH GLPVSQDKTQQTPGTIKFLGQIISPNHITYDAVPTVPIRSRWALPELQALLGEIQWVSKGTPTLRQPLHSLYCALQGHTDPRDQIYLNPSQVQSLMQLQ QALSQNCRSRLAQTLPLLGAIMLTLTGTTTVVFQSKQQWPLVWLHAPLPHTSQCPWGQLLASAVLLLDKYTLQSYGLLCQTIHHNISIQTFNQFIQTSD HPSVPILLHHSHRFKNLGAQTGELWNTFLKTAAPLAPVKALTPVFTLSPIIINTAPCLFSDGSTSQAAYILWDKHILSQRSFPLPPPHKSAQQAELLGLLH GLSSARSWHCLNIFLDSKYLYHYLRTLAWGTFQGKSSQAPFQALLPRLLAHKVIYLHHVRSHTNLPDPISKLNALTDALLITPIL HTL1L_P0C211_2mutB 8,037 GLEHLPRPPEISQFPLNPERLQALQHLVRKALEAGHIEPYTGPGNNPVFPVKKANGTWRFIHDLRATNSLTVDLSSSSPGPPDLSSPPTTLAHLQTIDLK DAFFQIPLPKQFQPYFAFTVPQQCNYGPGTRYAWKVLPQGFKNSPTLFQMQLASILQPIRQAFPQCVILQYMDDILLASPSPEDLQQLSEATMASLISH GLPVSQDKTQQTPGTIKFLGQIISPNHITYDAVPTVPIRSRWALPELQALLGEIQWVSKGTPTLRQPLHSLYCALQGHTDPRDQIYLNPSQVQSLMQLQ QALSQNCRSRLAQTLPLLGAIMLTLTGTTTVVFQSKQQWPLVWLHAPLPHTSQCPWGQLLASAVLLLDKYTLQSYGLLCQTIHHNISIQTFNQFIQTSD HPSVPILLHHSHRFKNLGAQTGELWNTFLKTAAPLAPVKALTPVFTLSPIIINTAPCLFSDGSTSQAAYILWDKHILSQRSFPLPPPHKSAQQAELLGLLH GLSSARSWHCLNIFLDSKYLYHYLRTLAWGTFQGKSSQAPFQALLPRLLAHKVIYLHHVRSHTNLPDPISKLNALTDALLITPIL HTL32_Q0R5R2 8,038 GLEHLPPPPEVSQFPLNPERLQALTDLVSRALEAKHIEPYQGPGNNPIFPVKKPNGKWRFIHDLRATNSVTRDLASPSPGPPDLTSLPQGLPHLRTIDLT DAFFQIPLPTIFQPYFAFTLPQPNNYGPGTRYSWRVLPQGFKNSPTLFEQQLSHILTPVRKTFPNSLIIQYMDDILLASPAPGELAALTDKVTNALTKEGL PLSPEKTQATPGPIHFLGQVISQDCITYETLPSINVKSTWSLAELQSMLGELQWVSKGTPVLRSSLHQLYLALRGHRDPRDTIKLTSIQVQALRTIQKALT LNCRSRLVNQLPILALIMLRPTGTTAVLFQTKQKWPLVWLHTPHPATSLRPWGQLLANAVIILDKYSLQHYGQVCKSFHHNISNQALTYYLHTSDQSSV AILLQHSHRFHNLGAQPSGPWRSLLQMPQIFQNIDVLRPPFTISPVVINHAPCLFSDGSASKAAFIIWDRQVIHQQVLSLPSTCSAQAGELFGLLAGLQK SQPWVALNIFLDSKFLIGHLRRMALGAFPGPSTQCELHTQLLPLLQGKTVYVHHVRSHTLLQDPISRLNEATDALMLAPLLPL HTL32_Q0R5R2_2mut 8,039 GLEHLPPPPEVSQFPLNPERLQALTDLVSRALEAKHIEPYQGPGNNPIFPVKKPNGKWRFIHDLRATNSVTRDLASPSPGPPDLTSLPQGLPHLRTIDLT DAFFQIPLPTIFQPYFAFTLPQPNNYGPGTRYSWRVLPQGFKNSPTLFQQQLSHILTPVRKTFPNSLIIQYMDDILLASPAPGELAALTDKVTNALTKEGL PLSPEKTQATPGPIHFLGQVISQDCITYETLPSINVKSTWSLAELQSMLGELQWVSKGTPVLRSSLHQLYLALRGHRDPRDTIKLTSIQVQALRTIQKALT LNCRSRLVNQLPILALIMLRPTGTTAVLFQTKQKWPLVWLHTPHPATSLRPWGQLLANAVIILDKYSLQHYGQVCKSFHHNISNQALTYYLHTSDQSSV AILLQHSHRFHNLGAQPSGPWRSLLQMPQIFQNIDVLRPPFTISPVVINHAPCLFSDGSASKAAFIIWDRQVIHQQVLSLPSTCSAQAGELFGLLAGLQK SQPWVALNIFLDSKFLIGHLRRMAWGAFPGPSTQCELHTQLLPLLQGKTVYVHHVRSHTLLQDPISRLNEATDALMLAPLLPL HTL32_Q0R5R2_2mutB 8,040 GLEHLPPPPEVSQFPLNPERLQALTDLVSRALEAKHIEPYQGPGNNPIFPVKKPNGKWRFIHDLRATNSVTRDLASPSPGPPDLTSPPQGLPHLRTIDL TDAFFQIPLPTIFQPYFAFTLPQPNNYGPGTRYSWRVLPQGFKNSPTLFQQQLSHILTPVRKTFPNSLIIQYMDDILLASPAPGELAALTDKVTNALTKEG LPLSPEKTQATPGPIHFLGQVISQDCITYETLPSINVKSTWSLAELQSMLGELQWVSKGTPVLRSSLHQLYLALRGHRDPRDTIKLTSIQVQALRTIQKAL TLNCRSRLVNQLPILALIMLRPTGTTAVLFQTKQKWPLVWLHTPHPATSLRPWGQLLANAVIILDKYSLQHYGQVCKSFHHNISNQALTYYLHTSDQSS VAILLQHSHRFHNLGAQPSGPWRSLLQMPQIFQNIDVLRPPFTISPVVINHAPCLFSDGSASKAAFIIWDRQVIHQQVLSLPSTCSAQAGELFGLLAGLQ KSQPWVALNIFLDSKFLIGHLRRMAWGAFPGPSTQCELHTQLLPLLQGKTVYVHHVRSHTLLQDPISRLNEATDALMLAPLLPL HTL3P_Q400X6 8,041 GLEHLPPPPEVSQFPLNPERLQALTDLVSRALEAKHIEPYQGPGNNPIFPVKKPNGKWRFIHDLRATNSLTRDLASPSPGPPDLTSLPQDLPHLRTIDLT DAFFQIPLPAVFQPYFAFTLPQPNNHGPGTRYSWRVLPQGFKNSPTLFEQQLSHILAPVRKAFPNSLIIQYMDDILLASPALRELTALTDKVTNALTKEGL PMSLEKTQATPGSIHFLGQVISPDCITYETLPSIHVKSIWSLAELQSMLGELQWVSKGTPVLRSSLHQLYLALRGHRDPRDTIELTSTQVQALKTIQKALA LNCRSRLVSQLPILALIILRPTGTTAVLFQTKQKWPLVWLHTPHPATSLRPWGQLLANAIITLDKYSLQHYGQICKSFHHNISNQALTYYLHTSDQSSVAIL LQHSHRFHNLGAQPSGPWRSLLQVPQIFQNIDVLRPPFIISPVVIDHAPCLFSDGATSKAAFILWDKQVIHQQVLPLPSTCSAQAGELFGLLAGLQKSKP WPALNIFLDSKFLIGHLRRMALGAFLGPSTQCDLHARLFPLLQGKTVYVHHVRSHTLLQDPISRLNEATDALMLAPLLPL HTL3P_Q400X6_2mut 8,042 GLEHLPPPPEVSQFPLNPERLQALTDLVSRALEAKHIEPYQGPGNNPIFPVKKPNGKWRFIHDLRATNSLTRDLASPSPGPPDLTSLPQDLPHLRTIDLT DAFFQIPLPAVFQPYFAFTLPQPNNHGPGTRYSWRVLPQGFKNSPTLFQQQLSHILAPVRKAFPNSLIIQYMDDILLASPALRELTALTDKVTNALTKEG LPMSLEKTQATPGSIHFLGQVISPDCITYETLPSIHVKSIWSLAELQSMLGELQWVSKGTPVLRSSLHQLYLALRGHRDPRDTIELTSTQVQALKTIQKAL ALNCRSRLVSQLPILALIILRPTGTTAVLFQTKQKWPLVWLHTPHPATSLRPWGQLLANAIITLDKYSLQHYGQICKSFHHNISNQALTYYLHTSDQSSVAI LLQHSHRFHNLGAQPSGPWRSLLQVPQIFQNIDVLRPPFIISPWVIDHAPCLFSDGATSKAAFILWDKQVIHQQVLPLPSTCSAQAGELFGLLAGLQKSK PWPALNIFLDSKFLIGHLRRMAWGAFLGPSTQCDLHARLFPLLQGKTVYVHHVRSHTLLQDPISRLNEATDALMLAPLLPL HTL3P_Q400X6_2mutB 8,043 GLEHLPPPPEVSQFPLNPERLQALTDLVSRALEAKHIEPYQGPGNNPIFPVKKPNGKWRFIHDLRATNSLTRDLASPSPGPPDLTSPPQDLPHLRTIDLT DAFFQIPLPAVFQPYFAFTLPQPNNHGPGTRYSWRVLPQGFKNSPTLFQQQLSHILAPVRKAFPNSLIIQYMDDILLASPALRELTALTDKVTNALTKEG LPMSLEKTQATPGSIHFLGQVISPDCITYETLPSIHVKSIWSLAELQSMLGELQWVSKGTPVLRSSLHQLYLALRGHRDPRDTIELTSTQVQALKTIQKAL ALNCRSRLVSQLPILALIILRPTGTTAVLFQTKQKWPLVWLHTPHPATSLRPWGQLLANAIITLDKYSLQHYGQICKSFHHNISNQALTYYLHTSDQSSVAI LLQHSHRFHNLGAQPSGPWRSLLQVPQIFQNIDVLRPPFIISPVVIDHAPCLFSDGATSKAAFILWDKQVIHQQVLPLPSTCSAQAGELFGLLAGLQKSK PWPALNIFLDSKFLIGHLRRMAWGAFLGPSTQCDLHARLFPLLQGKTVYVHHVRSHTLLQDPISRLNEATDALMLAPLLPL HTLV2_P03363_2mut 8,044 HLPPPPQVDQFPLNLPERLQALNDLVSKALEAGHIEPYSGPGNNPVFPVKKPNGKWRFIHDLRATNAITTTLTSPSPGPPDLTSLPTALPHLQTIDLTDA FFQIPLPKQYQPYFAFTIPQPCNYGPGTRYAWTVLPQGFKNSPTLFQQQLAAVLNPMRKMFPTSTIVQYMDDILLASPTNEELQQLSQLTLQALTTHGL PISQEKTQQTPGQIRFLGQVISPNHITYESTPTIPIKSQWTLTELQVILGEIQWVSKGTPILRKHLQSLYSALHPYRDPRACITLTPQQLHALHAIQQALQH NCRGRLNPALPLLGLISLSTSGTTSVIFQPKQNWPLAWLHTPHPPTSLCPWGHLLACTILTLDKYTLQHYGQLCQSFHHNMSKQALCDFLRNSPHPSV GILIHHMGRFHNLGSQPSGPWKTLLHLPTLLQEPRLLRPIFTLSPVVLDTAPCLFSDGSPQKAAYVLWDQTILQQDITPLPSHETHSAQKGELLALICGLR AAKPWPSLNIFLDSKYLIKYLHSLAIGAFLGTSAHQTLQAALPPLLQGKTIYLHHVRSHTNLPDPISTFNEYTDSLILAPLVPL JSRV_P31623 8,045 PLGTSDSPVTHADPIDWKSEEPVWVDQWPLTQEKLSAAQQLVQEQLRLGHIEPSTSAWNSPIFVIKKKSGKWRLLQDLRKVNETMMHMGALQPGLPT PSAIPDKSYIIVIDLKDCFYTIPLAPQDCKRFAFSLPSVNFKEPMQRYQWRVLPQGMTNSPTLCQKFVATAIAPVRQRFPQLYLVHYMDDILLAHTDEHLL YQAFSILKQHLSLNGLVIADEKIQTHFPYNYLGFSLYPRVYNTQLVKLQTDHLKTLNDFQKLLGDINWIRPYLKLPTYTLQPLFDILKGDSDPASPRTLSLE GRTALQSIEEAIRQQQITYCDYQRSWGLYILPTPRAPTGVLYQDKPLRWIYLSATPTKHLLPYYELVAKIIAKGRHEAIQYFGMEPPFICVPYALEQQDWL FQFSDNWSIAFANYPGQITHHYPSDKLLQFASSHAFIFPKIVRRQPIPEATLIFTDGSSNGTAALIINHQTYYAQTSFSSAQVVELFAVHQALLTVPTSFNL FTDSSYVVGALQMIETVPIIGTTSPEVLNLFTLIQQVLHCRQHPCFFGHIRAHSTLPGALVQGNHTADVLTKQVFFQS JSRV_P31623_2mutB 8,046 PLGTSDSPVTHADPIDWKSEEPVWVDQWPLTQEKLSAAQQLVQEQLRLGHIEPSTSAWNSPIFVIKKKSGKWRLLQDLRKVNETMMHMGALQPGLPT PSPIPDKSYIIVIDLKDCFYTIPLAPQDCKRFAFSLPSVNFKEPMQRYQWRVLPQGMTNSPTLCQKFVATAIAPVRQRFPQLYLVHYMDDILLAHTDEHLL YQAFSILKQHLSLNGLVIADEKIQTHFPYNYLGFSLYPRVYNTQLVKLQTDHLKTLNDFQKLLGDINWIRPYLKLPTYTLQPLFDILKGDSDPASPRTLSLE GRTALQSIEEAIRQQQITYCDYQRSWGLYILPTPRAPTGVLYQDKPLRWIYLSATPTKHLLPYYELVAKIIAKGRHEAIQYFGMEPPFICVPYALEQQDWL FQFSDNWSIAFANYPGQITHHYPSDKLLQFASSHAFIFPKIVRRQPIPEATLIFTDGSSNGTAALIINHQTYYAQTSFSSAQVVELFAVHQALLTVPTSFNL FTDSSYVVGALQMIETVPIIGTTSPEVLNLFTLIQQVLHCRQHPCFFGHIRAHSTLPGALVQGNHTADVLTKQVFFQS KORV_Q9TTC1 8,047 TLGDQGSRGSDPLPEPRVTLTVEGIPTEFLVNTGAEHSVLTKPMGKMGSKRTVVAGATGSKVYPWTTKRLLKIGQKQVTHSFLVIPECPAPLLGRDLLT KLKAQIQFSTEGPQVTWEDRPAMCLVLNLEEEYRLHEKPVPPSIDPSWLQLFPMVWAEKAGMGLANQVPPVVVELKSDASPVAVRQYPMSKEAREGI RPHIQRFLDLGILVPCQSPWNTPLLPVKKPGTNDYRPVQDLREVNKRVQDIHPTVPNPYNLLSSLPPSHTWYSVLDLKDAFFCLKLHPNSQPLFAFEW RDPEKGNTGQLTWTRLPQGFKNSPTLFDEALHRDLASFRALNPQVVMLQYVDDLLVAAPTYRDCKEGTRRLLQELSKLGYRVSAKKAQLCREEVTYL GYLLKGGKRWLTPARKATVMKIPTPTTPRQVREFLGTAGFCRLWIPGFASLAAPLYPLTREKVPFTWTEAHQEAFGRIKEALLSAPALALPDLTKPFAL YVDEKEGVARGVLTQTLGPWRRPVAYLSKKLDPVASGWPTCLKAIAAVALLLKDADKLTLGQNVLVIAPHNLESIVRQPPDRWMTNARMTHYQSLLLN ERVSFAPPAILNPATLLPVESDDTPIHICSEILAEETGTRPDLRDQPLPGVPAWYTDGSSFIMDGRRQAGAAIVDNKRTVWASNLPEGTSAQKAELIALT QALRLAEGKSINIYTDSRYAFATAHVHGAIYKQRGLLTSAGKDIKNKEEILALLEAIHLPKRVAIIHCPGHQRGTDPVATGNRKADEAAKQAAQSTRILTETTKN KORV_Q9TTC1_3mut 8,048 TLGDQGSRGSDPLPEPRVTLTVEGIPTEFLVNTGAEHSVLTKPMGKMGSKRTVVAGATGSKVYPWTTKRLLKIGQKQVTHSFLVIPECPAPLLGRDLLT KLKAQIQFSTEGPQVTWEDRPAMCLVLNLEEEYRLHEKPVPPSIDPSWLQLFPMVWAEKAGMGLANQVPPVVVELKSDASPVAVRQYPMSKEAREGI RPHIQRFLDLGILVPCQSPWNTPLLPVKKPGTNDYRPVQDLREVNKRVQDIHPTVPNPYNLLSSLPPSHTWYSVLDLKDAFFCLKLHPNSQPLFAFEW RDPEKGNTGQLTWTRLPQGFKNSPTLFNEALHRDLASFRALNPQVVMLQYVDDLLVAAPTYRDCKEGTRRLLQELSKLGYRVSAKKAQLCREEVTYL GYLLKGGKRWLTPARKATVMKIPTPTTPRQVREFLGTAGFCRLWIPGFASLAAPLYPLTRPKVPFTWTEAHQEAFGRIKEALLSAPALALPDLTKPFAL YVDEKEGVARGVLTQTLGPWRRPVAYLSKKLDPVASGWPTCLKAIAAVALLLKDADKLTLGQNVLVIAPHNLESIVRQPPDRWMTNARMTHYQSLLLN ERVSFAPPAILNPATLLPVESDDTPIHICSEILAEETGTRPDLRDQPLPGVPAWYTDGSSFIMDGRRQAGAAIVDNKRTVWASNLPEGTSAQKAELIALT QALRLAEGKSINIYTDSRYAFATAHVHGAIYKQRGWLTSAGKDIKNKEEILALLEAIHLPKRVAIIHCPGHQRGTDPVATGNRKADEAAKQAAQSTRILTETTKN KORV_Q9TTC1_3mutA 8,049 TLGDQGSRGSDPLPEPRVTLTVEGIPTEFLVNTGAEHSVLTKPMGKMGSKRTWVAGATGSKVYPWTTKRLLKIGQKQVTHSFLVIPECPAPLLGRDLLT KLKAQIQFSTEGPQVTWEDRPAMCLVLNLEEEYRLHEKPVPPSIDPSWLQLFPMVWAEKAGMGLANQVPPVVVELKSDASPVAVRQYPMSKEAREGI RPHIQRFLDLGILVPCQSPWNTPLLPVKKPGTNDYRPVQDLREVNKRVQDIHPTVPNPYNLLSSLPPSHTWYSVLDLKDAFFCLKLHPNSQPLFAFEW RDPEKGNTGQLTWTRLPQGFKNSPTLFNEALHRDLASFRALNPQVVMLQYVDDLLVAAPTYRDCKEGTRRLLQELSKLGYRVSAKKAQLCREEVTYL GYLLKGGKRWLTPARKATVMKIPTPTTPRQVREFLGKAGFCRLFIPGFASLAAPLYPLTRPKVPFTWTEAHQEAFGRIKEALLSAPALALPDLTKPFALY VDEKEGVARGVLTQTLGPWRRPVAYLSKKLDPVASGWPTCLKAIAAVALLLKDADKLTLGQNVLVIAPHNLESIVRQPPDRWMTNARMTHYQSLLLNE RVSFAPPAILNPATLLPVESDDTPIHICSEILAEETGTRPDLRDQPLPGVPAWYTDGSSFIMDGRRQAGAAIVDNKRTVWASNLPEGTSAQKAELIALTQ ALRLAEGKSINIYTDSRYAFATAHVHGAIYKQRGWLTSAGKDIKNKEEILALLEAIHLPKRVAIIHCPGHQRGTDPVATGNRKADEAAKQAAQSTRILTETTKN KORV_Q9TTC1-Pro 8,050 LLGRDLLTKLKAQIQFSTEGPQVTWEDRPAMCLVLNLEEEYRLHEKPVPPSIDPSWLQLFPMVWAEKAGMGLANQVPPVVVELKSDASPVAVRQYPM SKEAREGIRPHIQRFLDLGILVPCQSPWNTPLLPVKKPGTNDYRPVQDLREVNKRVQDIHPTVPNPYNLLSSLPPSHTWYSVLDLKDAFFCLKLHPNSQ PLFAFEWRDPEKGNTGQLTWTRLPQGFKNSPTLFDEALHRDLASFRALNPQWVMLQYVDDLLVAAPTYRDCKEGTRRLLQELSKLGYRVSAKKAQLC REEVTYLGYLLKGGKRWLTPARKATVMKIPTPTTPRQVREFLGTAGFCRLWIPGFASLAAPLYPLTREKVPFTWTEAHQEAFGRIKEALLSAPALALPD LTKPFALYVDEKEGVARGVLTQTLGPWRRPVAYLSKKLDPVASGWPTCLKAIAAVALLLKDADKLTLGQNVLVIAPHNLESIVRQPPDRWMTNARMTH YQSLLLNERVSFAPPAILNPATLLPVESDDTPIHICSEILAEETGTRPDLRDQPLPGVPAWYTDGSSFIMDGRRQAGAAIVDNKRTVWASNLPEGTSAQ KAELIALTQALRLAEGKSINIYTDSRYAFATAHVHGAIYKQRGLLTSAGKDIKNKEEILALLEAIHLPKRVAIIHCPGHQRGTDPVATGNRKADEAAKQAAQ STRILTETTKN KORV_Q9TTC1-Pro_3mut 8,051 LLGRDLLTKLKAQIQFSTEGPQVTWEDRPAMCLVLNLEEEYRLHEKPVPPSIDPSWLQLFPMVWAEKAGMGLANQVPPVVVELKSDASPVAVRQYPM SKEAREGIRPHIQRFLDLGILVPCQSPWNTPLLPVKKPGTNDYRPVQDLREVNKRVQDIHPTVPNPYNLLSSLPPSHTWYSVLDLKDAFFCLKLHPNSQ PLFAFEWRDPEKGNTGQLTWTRLPQGFKNSPTLFNEALHRDLASFRALNPQWVMLQYVDDLLVAAPTYRDCKEGTRRLLQELSKLGYRVSAKKAQLC REEVTYLGYLLKGGKRWLTPARKATVMKIPTPTTPRQVREFLGTAGFCRLWIPGFASLAAPLYPLTRPKVPFTWTEAHQEAFGRIKEALLSAPALALPD LTKPFALYVDEKEGVARGVLTQTLGPWRRPVAYLSKKLDPVASGWPTCLKAIAAVALLLKDADKLTLGQNVLVIAPHNLESIVRQPPDRWMTNARMTH YQSLLLNERVSFAPPAILNPATLLPVESDDTPIHICSEILAEETGTRPDLRDQPLPGVPAWYTDGSSFIMDGRRQAGAAIVDNKRTVWASNLPEGTSAQ KAELIALTQALRLAEGKSINIYTDSRYAFATAHVHGAIYKQRGWLTSAGKDIKNKEEILALLEAIHLPKRVAIIHCPGHQRGTDPVATGNRKADEAAKQAA QSTRILTETTKN KORV_Q9TTC1-Pro_3mutA 8,052 LLGRDLLTKLKAQIQFSTEGPQVTWEDRPAMCLVLNLEEEYRLHEKPVPPSIDPSWLQLFPMVWAEKAGMGLANQVPPVVVELKSDASPVAVRQYPM SKEAREGIRPHIQRFLDLGILVPCQSPWNTPLLPVKKPGTNDYRPVQDLREVNKRVQDIHPTVPNPYNLLSSLPPSHTWYSVLDLKDAFFCLKLHPNSQ PLFAFEWRDPEKGNTGQLTWTRLPQGFKNSPTLFNEALHRDLASFRALNPQVVMLQYVDDLLVAAPTYRDCKEGTRRLLQELSKLGYRVSAKKAQLC REEVTYLGYLLKGGKRWLTPARKATVMKIPTPTTPRQVREFLGKAGFCRLFIPGFASLAAPLYPLTRPKVPFTWTEAHQEAFGRIKEALLSAPALALPDL TKPFALYVDEKEGVARGVLTQTLGPWRRPVAYLSKKLDPVASGWPTCLKAIAAVALLLKDADKLTLGQNVLVIAPHNLESIVRQPPDRWMTNARMTHY QSLLLNERVSFAPPAILNPATLLPVESDDTPIHICSEILAEETGTRPDLRDQPLPGVPAWYTDGSSFIMDGRRQAGAAIVDNKRTVWASNLPEGTSAQK AELIALTQALRLAEGKSINIYTDSRYAFATAHVHGAIYKQRGWLTSAGKDIKNKEEILALLEAIHLPKRVAIIHCPGHQRGTDPVATGNRKADEAAKQAAQ STRILTETTKN MLVAV_P03356 8,053 TLNLEDEYRLYETSAEPEVSPGSTWLSDFPQAWAETGGMGLAVRQAPLIIPLKATSTPVSIKQYPMSQEAKLGIKPHIQRLLDQGILVPCQSPWNTPLL PVKKPGTNDYRPVQDLREVNKRVEDIHPTVPNPYNLLSGLPPSHRWYTVLDLKDAFFCLRLHPTSQPLFAFEWRDPGMGISGQLTWTRLPQGFKNSP TLFDEALHRDLADFRIQHPDLILLQYVDDILLAATSELDCQQGTRALLLTLGNLGYRASAKKAQLCQKQVKYLGYLLKEGQRWLTEARKETVMGQPTPK TPRQLREFLGTAGFCRLWIPGFAEMAAPLYPLTKTGTLFNWGPDQQKAYQEIKQALLTAPALGLPDLTKPFELFVDEKQGYAKGVLTQKLGPWRRPVA YLSKKLDPVAAGWPPCLRMVAAIAVLRKDAGKLTMGQPLVILAPHAVEALVKQPPDRWLSNARMTHYQAMLLDTDRVQFGPVVALNPATLLPLPEEG APHDCLEILAETHGTRPDLTDQPIPDADHTWYTDGSSFLQEGQRKAGAAVTTETEVIWARALPAGTSAQRAELIALTQALKMAEGKRLNVYTDSRYAF ATAHIHGEIYRRRGLLTSEGREIKNKSEILALLKALFLPKRLSIIHCLGHQKGDSAEARGNRLADQAAREAAIKTPPDTSTLL MLVAV_P03356_3mut 8,054 TLNLEDEYRLYETSAEPEVSPGSTWLSDFPQAWAETGGMGLAVRQAPLIIPLKATSTPVSIKQYPMSQEAKLGIKPHIQRLLDQGILVPCQSPWNTPLL PVKKPGTNDYRPVQDLREVNKRVEDIHPTVPNPYNLLSGLPPSHRWYTVLDLKDAFFCLRLHPTSQPLFAFEWRDPGMGISGQLTWTRLPQGFKNSP TLFNEALHRDLADFRIQHPDLILLQYVDDILLAATSELDCQQGTRALLLTLGNLGYRASAKKAQLCQKQVKYLGYLLKEGQRWLTEARKETVMGQPTPK TPRQLREFLGTAGFCRLWIPGFAEMAAPLYPLTKPGTLFNWGPDQQKAYQEIKQALLTAPALGLPDLTKPFELFVDEKQGYAKGVLTQKLGPWRRPV AYLSKKLDPVAAGWPPCLRMVAAIAVLRKDAGKLTMGQPLVILAPHAVEALVKQPPDRWLSNARMTHYQAMLLDTDRVQFGPWVALNPATLLPLPEE GAPHDCLEILAETHGTRPDLTDQPIPDADHTWYTDGSSFLQEGQRKAGAAVTTETEVIWARALPAGTSAQRAELIALTQALKMAEGKRLNVYTDSRYA FATAHIHGEIYRRRGWLTSEGREIKNKSEILALLKALFLPKRLSIIHCLGHQKGDSAEARGNRLADQAAREAAIKTPPDTSTLL MLVAV_P03356_3mutA 8,055 TLNLEDEYRLYETSAEPEVSPGSTWLSDFPQAWAETGGMGLAVRQAPLIIPLKATSTPVSIKQYPMSQEAKLGIKPHIQRLLDQGILVPCQSPWNTPLL PVKKPGTNDYRPVQDLREVNKRVEDIHPTVPNPYNLLSGLPPSHRWYTVLDLKDAFFCLRLHPTSQPLFAFEWRDPGMGISGQLTWTRLPQGFKNSP TLFNEALHRDLADFRIQHPDLILLQYVDDILLAATSELDCQQGTRALLLTLGNLGYRASAKKAQLCQKQVKYLGYLLKEGQRWLTEARKETVMGQPTPK TPRQLREFLGKAGFCRLFIPGFAEMAAPLYPLTKPGTLFNWGPDQQKAYQEIKQALLTAPALGLPDLTKPFELFVDEKQGYAKGVLTQKLGPWRRPVA YLSKKLDPVAAGWPPCLRMVAAIAVLRKDAGKLTMGQPLVILAPHAVEALVKQPPDRWLSNARMTHYQAMLLDTDRVQFGPWVALNPATLLPLPEEG APHDCLEILAETHGTRPDLTDQPIPDADHTWYTDGSSFLQEGQRKAGAAVTTETEVIWARALPAGTSAQRAELIALTQALKMAEGKRLNVYTDSRYAF ATAHIHGEIYRRRGWLTSEGREIKNKSEILALLKALFLPKRLSIIHCLGHQKGDSAEARGNRLADQAAREAAIKTPPDTSTLL MLVBM_Q7SVK7 8,056 TLGIEDEYRLHETSTEPDVSLGSTWLSDFPQAWAETGGMGLAVRQAPLIIPLKATSTPVSIQQYPMSHEARLGIKPHIQRLLDQGILVPCQSPWNTPLLP VKKPGTNDYRPVQDLREVNKRVEDIHPTVPNPYNLLSGLPPSHQWYTVLDLKDAFFCLRLHPTSQPLFAFEWRDPGMGISGQLTWTRLPQGFKNSPT LFDEALHRDLADFRIQHPDLILLQYVDDILLAATSELDCQQGTRALLQTLGDLGYRASAKKAQICQKQVKYLGYLLREGQRWLTEARKETVMGQPVPKT PRQLREFLGTAGFCRLWIPGFAEMAAPLYPLTKTGTLFSWGPDQQKAYQEIKQALLTAPALGLPDLTKPFELFVDEKQGYAKGVLTQKLGPWRRPVAY LSKKLDPVAAGWPPCLRMVAAIAVLTKDAGKLTMGQPLVILAPHAVEALVKQPPDRWLSNARMTHYQAMLLDTDRVQFGPWVALNPATLLPLPEEGAP HDCLEILAETHGTRPDLTDQPIPDADHTWYTDGSSFLQEGQRKAGAAVTTETEVIWAGALPAGTSAQRAELIALTQALKMAEGKRLNVYTDSRYAFAT AHIHGEIYRRRGLLTSEGREIKNKSEILALLKALFLPKRLSIIHCLGHQKGDSAEARGNRLADQAAREAAIKTPPDTSTLL MLVBM_Q7SVK7 8,057 TLGIEDEYRLHETSTEPDVSLGSTWLSDFPQAWAETGGMGLAVRQAPLIIPLKATSTPVSIQQYPMSHEARLGIKPHIQRLLDQGILVPCQSPWNTPLLP VKKPGTNDYRPVQDLREVNKRVEDIHPTVPNPYNLLSGLPPSHQWYTVLDLKDAFFCLRLHPTSQPLFAFEWRDPGMGISGQLTWTRLPQGFKNSPT LFDEALHRDLADFRIQHPDLILLQYVDDILLAATSELDCQQGTRALLQTLGDLGYRASAKKAQICQKQVKYLGYLLREGQRWLTEARKETVMGQPVPKT PRQLREFLGTAGFCRLWIPGFAEMAAPLYPLTKTGTLFSWGPDQQKAYQEIKQALLTAPALGLPDLTKPFELFVDEKQGYAKGVLTQKLGPWRRPVAY LSKKLDPVAAGWPPCLRMVAAIAVLTKDAGKLTMGQPLVILAPHAVEALVKQPPDRWLSNARMTHYQAMLLDTDRVQFGPWVALNPATLLPLPEEGAP HDCLEILAETHGTRPDLTDQPIPDADHTWYTDGSSFLQEGQRKAGAAVTTETEVIWAGALPAGTSAQRAELIALTQALKMAEGKRLNVYTDSRYAFAT AHIHGEIYRRRGLLTSEGREIKNKSEILALLKALFLPKRLSIIHCLGHQKGDSAEARGNRLADQAAREAAIKTPPDTSTLL MLVBM_Q7SVK7_3mut 8,058 TLGIEDEYRLHETSTEPDVSLGSTWLSDFPQAWAETGGMGLAVRQAPLIIPLKATSTPVSIQQYPMSHEARLGIKPHIQRLLDQGILVPCQSPWNTPLLP VKKPGTNDYRPVQDLREVNKRVEDIHPTVPNPYNLLSGLPPSHQWYTVLDLKDAFFCLRLHPTSQPLFAFEWRDPGMGISGQLTWTRLPQGFKNSPT LFNEALHRDLADFRIQHPDLILLQYVDDILLAATSELDCQQGTRALLQTLGDLGYRASAKKAQICQKQVKYLGYLLREGQRWLTEARKETVMGQPVPKT PRQLREFLGTAGFCRLWIPGFAEMAAPLYPLTKPGTLFSWGPDQQKAYQEIKQALLTAPALGLPDLTKPFELFVDEKQGYAKGVLTQKLGPWRRPVA YLSKKLDPVAAGWPPCLRMVAAIAVLTKDAGKLTMGQPLVILAPHAVEALVKQPPDRWLSNARMTHYQAMLLDTDRVQFGPWVALNPATLLPLPEEGA PHDCLEILAETHGTRPDLTDQPIPDADHTWYTDGSSFLQEGQRKAGAAVTTETEVIWAGALPAGTSAQRAELIALTQALKMAEGKRLNVYTDSRYAFA TAHIHGEIYRRRGWLTSEGREIKNKSEILALLKALFLPKRLSIIHCLGHQKGDSAEARGNRLADQAAREAAIKTPPDTSTLL MLVBM_Q7SVK7_3mut 8,059 TLGIEDEYRLHETSTEPDVSLGSTWLSDFPQAWAETGGMGLAVRQAPLIIPLKATSTPVSIQQYPMSHEARLGIKPHIQRLLDQGILVPCQSPWNTPLLP VKKPGTNDYRPVQDLREVNKRVEDIHPTVPNPYNLLSGLPPSHQWYTVLDLKDAFFCLRLHPTSQPLFAFEWRDPGMGISGQLTWTRLPQGFKNSPT LFNEALHRDLADFRIQHPDLILLQYVDDILLAATSELDCQQGTRALLQTLGDLGYRASAKKAQICQKQVKYLGYLLREGQRWLTEARKETVMGQPVPKT PRQLREFLGTAGFCRLWIPGFAEMAAPLYPLTKPGTLFSWGPDQQKAYQEIKQALLTAPALGLPDLTKPFELFVDEKQGYAKGVLTQKLGPWRRPVA YLSKKLDPVAAGWPPCLRMVAAIAVLTKDAGKLTMGQPLVILAPHAVEALVKQPPDRWLSNARMTHYQAMLLDTDRVQFGPVVALNPATLLPLPEEGA PHDCLEILAETHGTRPDLTDQPIPDADHTWYTDGSSFLQEGQRKAGAAVTTETEVIWAGALPAGTSAQRAELIALTQALKMAEGKRLNVYTDSRYAFA TAHIHGEIYRRRGWLTSEGREIKNKSEILALLKALFLPKRLSIIHCLGHQKGDSAEARGNRLADQAAREAAIKTPPDTSTLL MLVBM_Q7SVK7_3mutAWS 8,060 LGIEDEYRLHETSTEPDVSLGSTWLSDFPQAWAETGGMGLAVRQAPLIIPLKATSTPVSIQQYPMSHEARLGIKPHIQRLLDQGILVPCQSPWNTPLLPV KKPGTNDYRPVQDLREVNKRVEDIHPTVPNPYNLLSGLPPSHQWYTVLDLKDAFFCLRLHPTSQPLFAFEWRDPGMGISGQLTWTRLPQGFKNSPTL FNEALHRDLADFRIQHPDLILLQYVDDILLAATSELDCQQGTRALLQTLGDLGYRASAKKAQICQKQVKYLGYLLREGQRWLTEARKETVMGQPVPKTP RQLREFLGKAGFCRLFIPGFAEMAAPLYPLTKPGTLFSWGPDQQKAYQEIKQALLTAPALGLPDLTKPFELFVDEKQGYAKGVLTQKLGPWRRPVAYL SKKLDPVAAGWPPCLRMVAAIAVLTKDAGKLTMGQPLVILAPHAVEALVKQPPDRWLSNARMTHYQAMLLDTDRVQFGPWVALNPATLLPLPEEGAP HDCLEILAETHGTRPDLTDQPIPDADHTWYTDGSSFLQEGQRKAGAAVTTETEVIWAGALPAGTSAQRAELIALTQALKMAEGKRLNVYTDSRYAFAT AHIHGEIYRRRGWLTSEGREIKNKSEILALLKALFLPKRLSIIHCLGHQKGDSAEARGNRLADQAAREAAIKTPPDTSTLLI MLVBM_Q7SVK7_3mutAWS 8,061 LGIEDEYRLHETSTEPDVSLGSTWLSDFPQAWAETGGMGLAVRQAPLIIPLKATSTPVSIQQYPMSHEARLGIKPHIQRLLDQGILVPCQSPWNTPLLPV KKPGTNDYRPVQDLREVNKRVEDIHPTVPNPYNLLSGLPPSHQWYTVLDLKDAFFCLRLHPTSQPLFAFEWRDPGMGISGQLTWTRLPQGFKNSPTL FNEALHRDLADFRIQHPDLILLQYVDDILLAATSELDCQQGTRALLQTLGDLGYRASAKKAQICQKQVKYLGYLLREGQRWLTEARKETVMGQPVPKTP RQLREFLGKAGFCRLFIPGFAEMAAPLYPLTKPGTLFSWGPDQQKAYQEIKQALLTAPALGLPDLTKPFELFVDEKQGYAKGVLTQKLGPWRRPVAYL SKKLDPVAAGWPPCLRMVAAIAVLTKDAGKLTMGQPLVILAPHAVEALVKQPPDRWLSNARMTHYQAMLLDTDRVQFGPVVALNPATLLPLPEEGAP HDCLEILAETHGTRPDLTDQPIPDADHTWYTDGSSFLQEGQRKAGAAVTTETEVIWAGALPAGTSAQRAELIALTQALKMAEGKRLNVYTDSRYAFAT AHIHGEIYRRRGWLTSEGREIKNKSEILALLKALFLPKRLSIIHCLGHQKGDSAEARGNRLADQAAREAAIKTPPDTSTLLI MLVCB_P08361 8,062 TLNIEDEYRLHETSKEPDVSLGSTWLSDFPQAWAETGGMGLAVRQAPLIIPLKATSTPVSIKQYPMSQEARLGIKPHIQRLLDQGILVPCQSPWNTPLLP VKKPGTNDYRPVQDLREVNKRVEDIHPTVPNPYNLLSGLPPSHQWYTVLDLKDAFFCLRLHPTSQPLFAFEWRDPEMGISGQLTWTRLPQGFKNSPT LFDEALHRDLAGFRIQHPDLILLQYVDDLLLAATSELDCQQGTRALLQTLGDLGYRASAKKAQICQKQVKYLGYLLKEGQRWLTEARKETVMGQPIPKT PRQLREFLGTAGFCRLWIPGFAEMAAPLYPLTKTGTLFNWGPDQQKAFQEIKQALLTAPALGLPDLTKPFELFVDEKQGYAKGVLTQKLGPWRRPVAY LSKKLDPVAAGWPPCLRMVAAIAVLTKDAGKLTMGQPLVILAPHAVEALVKQPPDRWLSNARMTHYQALLLDTDRVQFGPVVALNPATLLPLPEEGLQ HDCLDILAEAHGTRSDLMDQPLPDADHTWYTDGSSFLQEGQRKAGAAVTTETEVIWARALPAGTSAQRAELIALTQALKMAEGKKLNVYTDSRYAFAT AHIHGEIYRRRGLLTSEGKEIKNKDEILALLKALFLPKRLSIIHCPGHQKGNSAEARGNRMADQAAREVATRETPETSTLL MLVCB_P08361_3mut 8,063 TLNIEDEYRLHETSKEPDVSLGSTWLSDFPQAWAETGGMGLAVRQAPLIIPLKATSTPVSIKQYPMSQEARLGIKPHIQRLLDQGILVPCQSPWNTPLLP VKKPGTNDYRPVQDLREVNKRVEDIHPTVPNPYNLLSGLPPSHQWYTVLDLKDAFFCLRLHPTSQPLFAFEWRDPEMGISGQLTWTRLPQGFKNSPT LFNEALHRDLAGFRIQHPDLILLQYVDDLLLAATSELDCQQGTRALLQTLGDLGYRASAKKAQICQKQVKYLGYLLKEGQRWLTEARKETVMGQPIPKT PRQLREFLGTAGFCRLWIPGFAEMAAPLYPLTKPGTLFNWGPDQQKAFQEIKQALLTAPALGLPDLTKPFELFVDEKQGYAKGVLTQKLGPWRRPVA YLSKKLDPVAAGWPPCLRMVAAIAVLTKDAGKLTMGQPLVILAPHAVEALVKQPPDRWLSNARMTHYQALLLDTDRVQFGPVVALNPATLLPLPEEGL QHDCLDILAEAHGTRSDLMDQPLPDADHTWYTDGSSFLQEGQRKAGAAVTTETEVIWARALPAGTSAQRAELIALTQALKMAEGKKLNVYTDSRYAF ATAHIHGEIYRRRGWLTSEGKEIKNKDEILALLKALFLPKRLSIIHCPGHQKGNSAEARGNRMADQAAREVATRETPETSTLL MLVCB_P08361_3mutA 8,064 TLNIEDEYRLHETSKEPDVSLGSTWLSDFPQAWAETGGMGLAVRQAPLIIPLKATSTPVSIKQYPMSQEARLGIKPHIQRLLDQGILVPCQSPWNTPLLP VKKPGTNDYRPVQDLREVNKRVEDIHPTVPNPYNLLSGLPPSHQWYTVLDLKDAFFCLRLHPTSQPLFAFEWRDPEMGISGQLTWTRLPQGFKNSPT LFNEALHRDLAGFRIQHPDLILLQYVDDLLLAATSELDCQQGTRALLQTLGDLGYRASAKKAQICQKQVKYLGYLLKEGQRWLTEARKETVMGQPIPKT PRQLREFLGKAGFCRLFIPGFAEMAAPLYPLTKPGTLFNWGPDQQKAFQEIKQALLTAPALGLPDLTKPFELFVDEKQGYAKGVLTQKLGPWRRPVAY LSKKLDPVAAGWPPCLRMVAAIAVLTKDAGKLTMGQPLVILAPHAVEALVKQPPDRWLSNARMTHYQALLLDTDRVQFGPVVALNPATLLPLPEEGLQ HDCLDILAEAHGTRSDLMDQPLPDADHTWYTDGSSFLQEGQRKAGAAVTTETEVIWARALPAGTSAQRAELIALTQALKMAEGKKLNVYTDSRYAFAT AHIHGEIYRRRGWLTSEGKEIKNKDEILALLKALFLPKRLSIIHCPGHQKGNSAEARGNRMADQAAREVATRETPETSTLL MLVF5_P26810 8,065 TLNIEDEYRLHETSKGPDVPLGSTWLSDFPQAWAETGGMGLAFRQAPLIISLKATSTPVSIKQYPMSQEARLGIKPHIQRLLDQGILVPCQSPWNTPLLP VKKPGTNDYRPVQDLREVNKRVEDIHPTVPNPYNLLSGLPPSHQWYTVLDLKDAFFCLRLHPTSQSLFAFEWKDPEMGISGQLTWTRLPQGFKNSPT LFDEALHRDLADFRIQHPDLILLQYVDDLLLAATSELDCQQGTRALLQTLGDLGYRASAKKAQICQKQVKYLGYLLKEGQRWLTEARKETVMGQPTPKT PRQLREFLGTAGLCRLWIPGFAEMAAPLYPLTKTGTLFKWGPDQQKAYQEIKQALLTAPALGLPDLTKPFELFVDEKQGYAKGVLTQKLGPWRRPVAY LSKKLDPVAAGWPPCLRMVAAIAVLTKDVGKLTMGQPLVILAPHAVEALVKQPPDRWLSNARMTHYQALLLDTDRVQFGPIVALNPATLLPLPEEGLQ HDCLDILAEAHGTRPDLTDQPLPDADHTWYTDGSSFLQEGQRRAGAAVTTETEVIWAKALPAGTSAQRAELIALTQALKMAAGKKLNVYTDSRYAFAT AHIHGEIYRRRGLLTSEGKEIKNKDEILALLKALFLPKRLSIIHCPGHQKGNHAEARGNRMADQAAREVATRETPETSTLL MLVF5_P26810_3mut 8,066 TLNIEDEYRLHETSKGPDVPLGSTWLSDFPQAWAETGGMGLAFRQAPLIISLKATSTPVSIKQYPMSQEARLGIKPHIQRLLDQGILVPCQSPWNTPLLP VKKPGTNDYRPVQDLREVNKRVEDIHPTVPNPYNLLSGLPPSHQWYTVLDLKDAFFCLRLHPTSQSLFAFEWKDPEMGISGQLTWTRLPQGFKNSPT LFNEALHRDLADFRIQHPDLILLQYVDDLLLAATSELDCQQGTRALLQTLGDLGYRASAKKAQICQKQVKYLGYLLKEGQRWLTEARKETVMGQPTPKT PRQLREFLGTAGLCRLWIPGFAEMAAPLYPLTKPGTLFKWGPDQQKAYQEIKQALLTAPALGLPDLTKPFELFVDEKQGYAKGVLTQKLGPWRRPVAY LSKKLDPVAAGWPPCLRMVAAIAVLTKDVGKLTMGQPLVILAPHAVEALVKQPPDRWLSNARMTHYQALLLDTDRVQFGPIVALNPATLLPLPEEGLQ HDCLDILAEAHGTRPDLTDQPLPDADHTWYTDGSSFLQEGQRRAGAAVTTETEVIWAKALPAGTSAQRAELIALTQALKMAAGKKLNVYTDSRYAFAT AHIHGEIYRRRGWLTSEGKEIKNKDEILALLKALFLPKRLSIIHCPGHQKGNHAEARGNRMADQAAREVATRETPETSTLL MLVF5_P26810_3mutA 8,067 TLNIEDEYRLHETSKGPDVPLGSTWLSDFPQAWAETGGMGLAFRQAPLIISLKATSTPVSIKQYPMSQEARLGIKPHIQRLLDQGILVPCQSPWNTPLLP VKKPGTNDYRPVQDLREVNKRVEDIHPTVPNPYNLLSGLPPSHQWYTVLDLKDAFFCLRLHPTSQSLFAFEWKDPEMGISGQLTWTRLPQGFKNSPT LFNEALHRDLADFRIQHPDLILLQYVDDLLLAATSELDCQQGTRALLQTLGDLGYRASAKKAQICQKQVKYLGYLLKEGQRWLTEARKETVMGQPTPKT PRQLREFLGKAGLCRLFIPGFAEMAAPLYPLTKPGTLFKWGPDQQKAYQEIKQALLTAPALGLPDLTKPFELFVDEKQGYAKGVLTQKLGPWRRPVAY LSKKLDPVAAGWPPCLRMVAAIAVLTKDVGKLTMGQPLVILAPHAVEALVKQPPDRWLSNARMTHYQALLLDTDRVQFGPIVALNPATLLPLPEEGLQ HDCLDILAEAHGTRPDLTDQPLPDADHTWYTDGSSFLQEGQRRAGAAVTTETEVIWAKALPAGTSAQRAELIALTQALKMAAGKKLNVYTDSRYAFAT AHIHGEIYRRRGWLTSEGKEIKNKDEILALLKALFLPKRLSIIHCPGHQKGNHAEARGNRMADQAAREVATRETPETSTLL MLVFF_P26809_3mut 8,068 TLNIEDEYRLHETSKGPDVPLGSTWLSDFPQAWAETGGMGLAVRQAPLIIPLKATSTPVSIKQYPMSQEARLGIKPHIQRLLDQGILVPCQSPWNTPLLP VKKPGTNDYRPVQDLREVNKRVEDIHPTVPNPYNLLSGLPPSHQWYTVLDLKDAFFCLRLHPTSQSLFAFEWRDPEMGISGQLTWTRLPQGFKNSPT LFNEALHRDLADFRIQHPDLILLQYVDDLLLAATSELDCQQGTRALLQTLGDLGYRASAKKAQICQKQVKYLGYLLKEGQRWLTEARKETVMGQPTPKT PRQLREFLGTAGFCRLWIPGFAEMAAPLYPLTKPGTLFEWGPDQQKAYQEIKQALLTAPALGLPDLTKPFELFVDEKQGYAKGVLTQKLGPWRRPVA YLSKKLDPVAAGWPPCLRMVAAIAVLTKDAGKLTMGQPLVILAPHAVEALVKQPPDRWLSNARMTHYQALLLDTDRVQFGPIVALNPATLLPLPEEGLQ HDCLDILAEAHGTRPDLTDQPLPDADHTWYTDGSSFLQEGQRKAGAAVTTETEVVWAKALPAGTSAQRAELIALTQALKMAEGKKLNVYTDSRYAFA TAHIHGEIYRRRGWLTSEGKEIKNKDEILALLKALFLPKRLSIIHCPGHQKGNRAEARGNRMADQAAREVATRETPETSTLL MLVFF_P26809_3mutA 8,069 TLNIEDEYRLHETSKGPDVPLGSTWLSDFPQAWAETGGMGLAVRQAPLIIPLKATSTPVSIKQYPMSQEARLGIKPHIQRLLDQGILVPCQSPWNTPLLP VKKPGTNDYRPVQDLREVNKRVEDIHPTVPNPYNLLSGLPPSHQWYTVLDLKDAFFCLRLHPTSQSLFAFEWRDPEMGISGQLTWTRLPQGFKNSPT LFNEALHRDLADFRIQHPDLILLQYVDDLLLAATSELDCQQGTRALLQTLGDLGYRASAKKAQICQKQVKYLGYLLKEGQRWLTEARKETVMGQPTPKT PRQLREFLGKAGFCRLFIPGFAEMAAPLYPLTKPGTLFEWGPDQQKAYQEIKQALLTAPALGLPDLTKPFELFVDEKQGYAKGVLTQKLGPWRRPVAY LSKKLDPVAAGWPPCLRMVAAIAVLTKDAGKLTMGQPLVILAPHAVEALVKQPPDRWLSNARMTHYQALLLDTDRVQFGPIVALNPATLLPLPEEGLQ HDCLDILAEAHGTRPDLTDQPLPDADHTWYTDGSSFLQEGQRKAGAAVTTETEVWAKALPAGTSAQRAELIALTQALKMAEGKKLNVYTDSRYAFA TAHIHGEIYRRRGWLTSEGKEIKNKDEILALLKALFLPKRLSIIHCPGHQKGNRAEARGNRMADQAAREVATRETPETSTLL MLVMS_P03355 8,070 TLNIEDEHRLHETSKEPDVSLGSTWLSDFPQAWAETGGMGLAVRQAPLIIPLKATSTPVSIKQYPMSQEARLGIKPHIQRLLDQGILVPCQSPWNTPLLP VKKPGTNDYRPVQDLREVNKRVEDIHPTVPNPYNLLSGLPPSHQWYTVLDLKDAFFCLRLHPTSQPLFAFEWRDPEMGISGQLTWTRLPQGFKNSPT LFDEALHRDLADFRIQHPDLILLQYVDDLLLAATSELDCQQGTRALLQTLGNLGYRASAKKAQICQKQVKYLGYLLKEGQRWLTEARKETVMGQPTPKT PRQLREFLGTAGFCRLWIPGFAEMAAPLYPLTKTGTLFNWGPDQQKAYQEIKQALLTAPALGLPDLTKPFELFVDEKQGYAKGVLTQKLGPWRRPVA YLSKKLDPVAAGWPPCLRMVAAIAVLTKDAGKLTMGQPLVILAPHAVEALVKQPPDRWLSNARMTHYQALLLDTDRVQFGPWVALNPATLLPLPEEGL QHNCLDILAEAHGTRPDLTDQPLPDADHTWYTDGSSLLQEGQRKAGAAVTTETEVIWAKALPAGTSAQRAELIALTQALKMAEGKKLNVYTDSRYAFA TAHIHGEIYRRRGLLTSEGKEIKNKDEILALLKALFLPKRLSIIHCPGHQKGHSAEARGNRMADQAARKAAITETPDTSTLL MLVMS_reference 8,137 TLNIEDEYRLHETSKEPDVSLGSTWLSDFPQAWAETGGMGLAVRQAPLIIPLKATSTPVSIKQYPMSQEARLGIKPHIQRLLDQGILVPCQSPWNTPLLP VKKPGTNDYRPVQDLREVNKRVEDIHPTVPNPYNLLSGLPPSHQWYTVLDLKDAFFCLRLHPTSQPLFAFEWRDPEMGISGQLTWTRLPQGFKNSPT LFNEALHRDLADFRIQHPDLILLQYVDDLLLAATSELDCQQGTRALLQTLGNLGYRASAKKAQICQKQVKYLGYLLKEGQRWLTEARKETVMGQPTPKT PRQLREFLGKAGFCRLFIPGFAEMAAPLYPLTKPGTLFNWGPDQQKAYQEIKQALLTAPALGLPDLTKPFELFVDEKQGYAKGVLTQKLGPWRRPVAY LSKKLDPVAAGWPPCLRMVAAIAVLTKDAGKLTMGQPLVILAPHAVEALVKQPPDRWLSNARMTHYQALLLDTDRVQFGPVVALNPATLLPLPEEGLQ HNCLDILAEAHGTRPDLTDQPLPDADHTWYTDGSSLLQEGQRKAGAAVTTETEVIWAKALPAGTSAQRAELIALTQALKMAEGKKLNVYTDSRYAFAT AHIHGEIYRRRGWLTSEGKEIKNKDEILALLKALFLPKRLSIIHCPGHQKGHSAEARGNRMADQAARKAAITETPDTSTLLIENSSP MLVMS_P03355 8,071 TLNIEDEHRLHETSKEPDVSLGSTWLSDFPQAWAETGGMGLAVRQAPLIIPLKATSTPVSIKQYPMSQEARLGIKPHIQRLLDQGILVPCQSPWNTPLLP VKKPGTNDYRPVQDLREVNKRVEDIHPTVPNPYNLLSGLPPSHQWYTVLDLKDAFFCLRLHPTSQPLFAFEWRDPEMGISGQLTWTRLPQGFKNSPT LFDEALHRDLADFRIQHPDLILLQYVDDLLLAATSELDCQQGTRALLQTLGNLGYRASAKKAQICQKQVKYLGYLLKEGQRWLTEARKETVMGQPTPKT PRQLREFLGTAGFCRLWIPGFAEMAAPLYPLTKTGTLFNWGPDQQKAYQEIKQALLTAPALGLPDLTKPFELFVDEKQGYAKGVLTQKLGPWRRPVA YLSKKLDPVAAGWPPCLRMVAAIAVLTKDAGKLTMGQPLVILAPHAVEALVKQPPDRWLSNARMTHYQALLLDTDRVQFGPVVALNPATLLPLPEEGL QHNCLDILAEAHGTRPDLTDQPLPDADHTWYTDGSSLLQEGQRKAGAAVTTETEVIWAKALPAGTSAQRAELIALTQALKMAEGKKLNVYTDSRYAFA TAHIHGEIYRRRGLLTSEGKEIKNKDEILALLKALFLPKRLSIIHCPGHQKGHSAEARGNRMADQAARKAAITETPDTSTLL MLVMS_P03355_3mut 8,072 TLNIEDEHRLHETSKEPDVSLGSTWLSDFPQAWAETGGMGLAVRQAPLIIPLKATSTPVSIKQYPMSQEARLGIKPHIQRLLDQGILVPCQSPWNTPLLP VKKPGTNDYRPVQDLREVNKRVEDIHPTVPNPYNLLSGLPPSHQWYTVLDLKDAFFCLRLHPTSQPLFAFEWRDPEMGISGQLTWTRLPQGFKNSPT LFNEALHRDLADFRIQHPDLILLQYVDDLLLAATSELDCQQGTRALLQTLGNLGYRASAKKAQICQKQVKYLGYLLKEGQRWLTEARKETVMGQPTPKT PRQLREFLGTAGFCRLWIPGFAEMAAPLYPLTKPGTLFNWGPDQQKAYQEIKQALLTAPALGLPDLTKPFELFVDEKQGYAKGVLTQKLGPWRRPVA YLSKKLDPVAAGWPPCLRMVAAIAVLTKDAGKLTMGQPLVILAPHAVEALVKQPPDRWLSNARMTHYQALLLDTDRVQFGPWVALNPATLLPLPEEGL QHNCLDILAEAHGTRPDLTDQPLPDADHTWYTDGSSLLQEGQRKAGAAVTTETEVIWAKALPAGTSAQRAELIALTQALKMAEGKKLNVYTDSRYAFA TAHIHGEIYRRRGWLTSEGKEIKNKDEILALLKALFLPKRLSIIHCPGHQKGHSAEARGNRMADQAARKAAITETPDTSTLL MLVMS_P03355_3mut 8,073 TLNIEDEHRLHETSKEPDVSLGSTWLSDFPQAWAETGGMGLAVRQAPLIIPLKATSTPVSIKQYPMSQEARLGIKPHIQRLLDQGILVPCQSPWNTPLLP VKKPGTNDYRPVQDLREVNKRVEDIHPTVPNPYNLLSGLPPSHQWYTVLDLKDAFFCLRLHPTSQPLFAFEWRDPEMGISGQLTWTRLPQGFKNSPT LFNEALHRDLADFRIQHPDLILLQYVDDLLLAATSELDCQQGTRALLQTLGNLGYRASAKKAQICQKQVKYLGYLLKEGQRWLTEARKETVMGQPTPKT PRQLREFLGTAGFCRLWIPGFAEMAAPLYPLTKPGTLFNWGPDQQKAYQEIKQALLTAPALGLPDLTKPFELFVDEKQGYAKGVLTQKLGPWRRPVA YLSKKLDPVAAGWPPCLRMVAAIAVLTKDAGKLTMGQPLVILAPHAVEALVKQPPDRWLSNARMTHYQALLLDTDRVQFGPVVALNPATLLPLPEEGL QHNCLDILAEAHGTRPDLTDQPLPDADHTWYTDGSSLLQEGQRKAGAAVTTETEVIWAKALPAGTSAQRAELIALTQALKMAEGKKLNVYTDSRYAFA TAHIHGEIYRRRGWLTSEGKEIKNKDEILALLKALFLPKRLSIIHCPGHQKGHSAEARGNRMADQAARKAAITETPDTSTLL MLVMS_P03355_3mutAWS 8,074 TLNIEDEHRLHETSKEPDVSLGSTWLSDFPQAWAETGGMGLAVRQAPLIIPLKATSTPVSIKQYPMSQEARLGIKPHIQRLLDQGILVPCQSPWNTPLLP VKKPGTNDYRPVQDLREVNKRVEDIHPTVPNPYNLLSGLPPSHQWYTVLDLKDAFFCLRLHPTSQPLFAFEWRDPEMGISGQLTWTRLPQGFKNSPT LFNEALHRDLADFRIQHPDLILLQYVDDLLLAATSELDCQQGTRALLQTLGNLGYRASAKKAQICQKQVKYLGYLLKEGQRWLTEARKETVMGQPTPKT PRQLREFLGKAGFCRLFIPGFAEMAAPLYPLTKPGTLFNWGPDQQKAYQEIKQALLTAPALGLPDLTKPFELFVDEKQGYAKGVLTQKLGPWRRPVAY LSKKLDPVAAGWPPCLRMVAAIAVLTKDAGKLTMGQPLVILAPHAVEALVKQPPDRWLSNARMTHYQALLLDTDRVQFGPVVALNPATLLPLPEEGLQ HNCLDILAEAHGTRPDLTDQPLPDADHTWYTDGSSLLQEGQRKAGAAVTTETEVIWAKALPAGTSAQRAELIALTQALKMAEGKKLNVYTDSRYAFAT AHIHGEIYRRRGWLTSEGKEIKNKDEILALLKALFLPKRLSIIHCPGHQKGHSAEARGNRMADQAARKAAITETPDTSTLL MLVMS_P03355_3mutAWS 8,075 TLNIEDEHRLHETSKEPDVSLGSTWLSDFPQAWAETGGMGLAVRQAPLIIPLKATSTPVSIKQYPMSQEARLGIKPHIQRLLDQGILVPCQSPWNTPLLP VKKPGTNDYRPVQDLREVNKRVEDIHPTVPNPYNLLSGLPPSHQWYTVLDLKDAFFCLRLHPTSQPLFAFEWRDPEMGISGQLTWTRLPQGFKNSPT LFNEALHRDLADFRIQHPDLILLQYVDDLLLAATSELDCQQGTRALLQTLGNLGYRASAKKAQICQKQVKYLGYLLKEGQRWLTEARKETVMGQPTPKT PRQLREFLGKAGFCRLFIPGFAEMAAPLYPLTKPGTLFNWGPDQQKAYQEIKQALLTAPALGLPDLTKPFELFVDEKQGYAKGVLTQKLGPWRRPVAY LSKKLDPVAAGWPPCLRMVAAIAVLTKDAGKLTMGQPLVILAPHAVEALVKQPPDRWLSNARMTHYQALLLDTDRVQFGPWVALNPATLLPLPEEGLQ HNCLDILAEAHGTRPDLTDQPLPDADHTWYTDGSSLLQEGQRKAGAAVTTETEVIWAKALPAGTSAQRAELIALTQALKMAEGKKLNVYTDSRYAFAT AHIHGEIYRRRGWLTSEGKEIKNKDEILALLKALFLPKRLSIIHCPGHQKGHSAEARGNRMADQAARKAAITETPDTSTLL MLVMS_P03355_PLV919 8,076 TLNIEDEYRLHETSKEPDVSLGSTWLSDFPQAWAETGGMGLAVRQAPLIIPLKATSTPVSIKQYPMSQEARLGIKPHIQRLLDQGILVPCQSPWNTPLLP VKKPGTNDYRPVQDLREVNKRVEDIHPTVPNPYNLLSGLPPSHQWYTVLDLKDAFFCLRLHPTSQPLFAFEWRDPEMGISGQLTWTRLPQGFKNSPT LFNEALHRDLADFRIQHPDLILLQYVDDLLLAATSELDCQQGTRALLQTLGNLGYRASAKKAQICQKQVKYLGYLLKEGQRWLTEARKETVMGQPTPKT PRQLREFLGKAGFCRLFIPGFAEMAAPLYPLTKPGTLFNWGPDQQKAYQEIKQALLTAPALGLPDLTKPFELFVDEKQGYAKGVLTQKLGPWRRPVAY LSKKLDPVAAGWPPCLRMVAAIAVLTKDAGKLTMGQPLVILAPHAVEALVKQPPDRWLSNARMTHYQALLLDTDRVQFGPWVALNPATLLPLPEEGLQ HNCLDILAEAHGTRPDLTDQPLPDADHTWYTDGSSLLQEGQRKAGAAVTTETEVIWAKALPAGTSAQRAELIALTQALKMAEGKKLNVYTDSRYAFAT AHIHGEIYRRRGWLTSEGKEIKNKDEILALLKALFLPKRLSIIHCPGHQKGHSAEARGNRMADQAARKAAITETPDTSTLLIENSSPSGGSKRTADGSEFE MLVMS_P03355_PLV919 8,077 TLNIEDEYRLHETSKEPDVSLGSTWLSDFPQAWAETGGMGLAVRQAPLIIPLKATSTPVSIKQYPMSQEARLGIKPHIQRLLDQGILVPCQSPWNTPLLP VKKPGTNDYRPVQDLREVNKRVEDIHPTVPNPYNLLSGLPPSHQWYTVLDLKDAFFCLRLHPTSQPLFAFEWRDPEMGISGQLTWTRLPQGFKNSPT LFNEALHRDLADFRIQHPDLILLQYVDDLLLAATSELDCQQGTRALLQTLGNLGYRASAKKAQICQKQVKYLGYLLKEGQRWLTEARKETVMGQPTPKT PRQLREFLGKAGFCRLFIPGFAEMAAPLYPLTKPGTLFNWGPDQQKAYQEIKQALLTAPALGLPDLTKPFELFVDEKQGYAKGVLTQKLGPWRRPVAY LSKKLDPVAAGWPPCLRMVAAIAVLTKDAGKLTMGQPLVILAPHAVEALVKQPPDRWLSNARMTHYQALLLDTDRVQFGPVVALNPATLLPLPEEGLQ HNCLDILAEAHGTRPDLTDQPLPDADHTWYTDGSSLLQEGQRKAGAAVTTETEVIWAKALPAGTSAQRAELIALTQALKMAEGKKLNVYTDSRYAFAT AHIHGEIYRRRGWLTSEGKEIKNKDEILALLKALFLPKRLSIIHCPGHQKGHSAEARGNRMADQAARKAAITETPDTSTLLIENSSPSGGSKRTADGSEFE MLVRD_P11227 8,078 TLNIEDEYRLHEISTEPDVSPGSTWLSDFPQAWAETGGMGLAVRQAPLIIPLKATSTPVSIKQYPMSQEAKLGIKPHIQRLLDQGILVPCQSPWNTPLLP VKKPGTNDYRPVQGLREVNKRVEDIHPTVPNPYNLLSGLPTSHRWYTVLDLKDAFFCLRLHPTSQPLFASEWRDPGMGISGQLTWTRLPQGFKNSPT LFDEALHRGLADFRIQHPDLILLQYVDDLLLAATSELDCQQGTRALLKTLGNLGYRASAKKAQICQKQVKYLGYLLREGQRWLTEARKETVMGQPTPKT PRQLREFLGTAGFCRLWIPRFAEMAAPLYPLTKTGTLFNWGPDQQKAYHEIKQALLTAPALGLPDLTKPFELFVDEKQGYAKGVLTQKLGPWRRPVAY LSKKLDPVAAGWPPCLRMVAAIAVLTKDAGKLTMGQPLVILAPHAVEALVKQPPDRWLSNARMTHYQAMLLDTDRVQFGPVVALNPATLLPLPEEGAP HDCLEILAETHGTEPDLTDQPIPDADHTWYTDGSSFLQEGQRKAGAAVTTETEVIWARALPAGTSAQRAELIALTQALKMAEGKRLNVYTDSRYAFATA HIHGEIYKRRGLLTSEGREIKNKSEILALLKALFLPKRLSIIHCLGHQKGDSAEARGNRLADQAAREAAIKTPPDTSTLL MLVRD_P11227_3mut 8,079 TLNIEDEYRLHEISTEPDVSPGSTWLSDFPQAWAETGGMGLAVRQAPLIIPLKATSTPVSIKQYPMSQEAKLGIKPHIQRLLDQGILVPCQSPWNTPLLP VKKPGTNDYRPVQGLREVNKRVEDIHPTVPNPYNLLSGLPTSHRWYTVLDLKDAFFCLRLHPTSQPLFASEWRDPGMGISGQLTWTRLPQGFKNSPT LFNEALHRGLADFRIQHPDLILLQYVDDLLLAATSELDCQQGTRALLKTLGNLGYRASAKKAQICQKQVKYLGYLLREGQRWLTEARKETVMGQPTPKT PRQLREFLGTAGFCRLWIPRFAEMAAPLYPLTKPGTLFNWGPDQQKAYHEIKQALLTAPALGLPDLTKPFELFVDEKQGYAKGVLTQKLGPWRRPVAY LSKKLDPVAAGWPPCLRMVAAIAVLTKDAGKLTMGQPLVILAPHAVEALVKQPPDRWLSNARMTHYQAMLLDTDRVQFGPWVALNPATLLPLPEEGAP HDCLEILAETHGTEPDLTDQPIPDADHTWYTDGSSFLQEGQRKAGAAVTTETEVIWARALPAGTSAQRAELIALTQALKMAEGKRLNVYTDSRYAFATA HIHGEIYKRRGWLTSEGREIKNKSEILALLKALFLPKRLSIIHCLGHQKGDSAEARGNRLADQAAREAAIKTPPDTSTLL MMTVB_P03365 8,080 WVQEISDSRPMLHIYLNGRRFLGLLNTGADKTCIAGRDWPANWPIHQTESSLQGLGMACGVARSSQPLRWQHEDKSGIIHPFVIPTLPFTLWGRDIMK DIKVRLMTDSPDDSQDLMIGAIESNLFADQISWKSDQPVWLNQWPLKQEKLQALQQLVTEQLQLGHLEESNSPWNTPVFVIKKKSGKWRLLQDLRAV NATMHDMGALQPGLPSPVAVPKGWEIIIIDLQDCFFNIKLHPEDCKRFAFSVPSPNFKRPYQRFQWKVLPQGMKNSPTLCQKFVDKAILTVRDKYQDS YIVHYMDDILLAHPSRSIVDEILTSMIQALNKHGLVVSTEKIQKYDNLKYLGTHIQGDSVSYQKLQIRTDKLRTLNDFQKLLGNINWIRPFLKLTTGELKPLF EILNGDSNPISTRKLTPEACKALQLMNERLSTARVKRLDLSQPWSLCILKTEYTPTACLWQDGVVEWIHLPHISPKVITPYDIFCTQLIIKGRHRSKELFSK DPDYIVVPYTKVQFDLLLQEKEDWPISLLGFLGEVHFHLPKDPLLTFTLQTAIIFPHMTSTTPLEKGIVIFTDGSANGRSVTYIQGREPIIKENTQNTAQQA EIVAVITAFEEVSQPFNLYTDSKYVTGLFPEIETATLSPRTKIYTELKHLQRLIHKRQEKFYIGHIRGHTGLPGPLAQGNAYADSLTRILT MMTVB_P03365 8,081 WVQEISDSRPMLHIYLNGRRFLGLLNTGADKTCIAGRDWPANWPIHQTESSLQGLGMACGVARSSQPLRWQHEDKSGIIHPFVIPTLPFTLWGRDIMK DIKVRLMTDSPDDSQDLMIGAIESNLFADQISWKSDQPVWLNQWPLKQEKLQALQQLVTEQLQLGHLEESNSPWNTPVFVIKKKSGKWRLLQDLRAV NATMHDMGALQPGLPSPVAVPKGWEIIIIDLQDCFFNIKLHPEDCKRFAFSVPSPNFKRPYQRFQWKVLPQGMKNSPTLCQKFVDKAILTVRDKYQDS YIVHYMDDILLAHPSRSIVDEILTSMIQALNKHGLVVSTEKIQKYDNLKYLGTHIQGDSVSYQKLQIRTDKLRTLNDFQKLLGNINWIRPFLKLTTGELKPLF EILNGDSNPISTRKLTPEACKALQLMNERLSTARVKRLDLSQPWSLCILKTEYTPTACLWQDGVVEWIHLPHISPKVITPYDIFCTQLIIKGRHRSKELFSK DPDYIVVPYTKVQFDLLLQEKEDWPISLLGFLGEVHFHLPKDPLLTFTLQTAIIFPHMTSTTPLEKGIVIFTDGSANGRSVTYIQGREPIIKENTQNTAQQA EIVAVITAFEEVSQPFNLYTDSKYVTGLFPEIETATLSPRTKIYTELKHLQRLIHKRQEKFYIGHIRGHTGLPGPLAQGNAYADSLTRILT MMTVB_P03365_2mut 8,082 WVQEISDSRPMLHIYLNGRRFLGLLNTGADKTCIAGRDWPANWPIHQTESSLQGLGMACGVARSSQPLRWQHEDKSGIIHPFVIPTLPFTLWGRDIMK DIKVRLMTDSPDDSQDLMIGAIESNLFADQISWKSDQPVWLNQWPLKQEKLQALQQLVTEQLQLGHLEESNSPWNTPVFVIKKKSGKWRLLQDLRAV NATMHDMGALQPGLPSPVAVPKGWEIIIIDLQDCFFNIKLHPEDCKRFAFSVPSPNFKRPYQRFQWKVLPQGMKNSPTLCQKFVDKAILTVRDKYQDS YIVHYMDDILLAHPSRSIVDEILTSMIQALNKHGLVVSTEKIQKYDNLKYLGTHIQGDSVSYQKLQIRTDKLRTLNDFQKLLGNINWIRPFLKLTTGELKPLF EILNPDSNPISTRKLTPEACKALQLMNERLSTARVKRLDLSQPWSLCILKTEYTPTACLWQDGVVEWIHLPHISPKVITPYDIFCTQLIIKGRHRSKELFSK DPDYIVVPYTKVQFDLLLQEKEDWPISLLGFLGEVHFHLPKDPLLTFTLQTAIIFPHMTSTTPLEKGIVIFTDGSANGRSVTYIQGREPIIKENTQNTAQQA EIVAVITAFEEVSQPFNLYTDSKYVTGLFPEIETATLSPRTKIYTELKHLQRLIHKRQEKFYIGHIRGHTGLPGPLAQGNAYADSLTRILT MMTVB_P03365_2mut_WS 8,083 VQEISDSRPMLHIYLNGRRFLGLLDTGADKTCIAGRDWPANWPIHQTESSLQGLGMACGVARSSQPLRWQHEDKSGIIHPFVIPTLPFTLWGRDIMKDI KVRLMTDSPDDSQDLMIGAIESNLFADQISWKSDQPVWLNQWPLKQEKLQALQQLVTEQLQLGHLEESNSPWNTPVFVIKKKSGKWRLLQDLRAVNA TMHDMGALQPGLPSPVAVPKGWEIIIIDLQDCFFNIKLHPEDCKRFAFSVPSPNFKRPYQRFQWKVLPQGMKNSPTLCQKFVDKAILTVRDKYQDSYIV HYMDDILLAHPSRSIVDEILTSMIQALNKHGLVVSTEKIQKYDNLKYLGTHIQGDSVSYQKLQIRTDKLRTLNDFQKLLGNINWIRPFLKLTTGELKPLFEIL NPDSNPISTRKLTPEACKALQLMNERLSTARVKRLDLSQPWSLCILKTEYTPTACLWQDGVVEWIHLPHISPKVITPYDIFCTQLIIKGRHRSKELFSKDP DYIVVPYTKVQFDLLLQEKEDWPISLLGFLGEVHFHLPKDPLLTFTLQTAIIFPHMTSTTPLEKGIVIFTDGSANGRSVTYIQGREPIIKENTQNTAQQAEIV AVITAFEEVSQPFNLYTDSKYVTGLFPEIETATLSPRTKIYTELKHLQRLIHKRQEKFYIGHIRGHTGLPGPLAQGNAYADSLTRILTA MMTVB_P03365_2mut_WS 8,084 VQEISDSRPMLHIYLNGRRFLGLLDTGADKTCIAGRDWPANWPIHQTESSLQGLGMACGVARSSQPLRWQHEDKSGIIHPFVIPTLPFTLWGRDIMKDI KVRLMTDSPDDSQDLMIGAIESNLFADQISWKSDQPVWLNQWPLKQEKLQALQQLVTEQLQLGHLEESNSPWNTPVFVIKKKSGKWRLLQDLRAVNA TMHDMGALQPGLPSPVAVPKGWEIIIIDLQDCFFNIKLHPEDCKRFAFSVPSPNFKRPYQRFQWKVLPQGMKNSPTLCQKFVDKAILTVRDKYQDSYIV HYMDDILLAHPSRSIVDEILTSMIQALNKHGLVVSTEKIQKYDNLKYLGTHIQGDSVSYQKLQIRTDKLRTLNDFQKLLGNINWIRPFLKLTTGELKPLFEIL NPDSNPISTRKLTPEACKALQLMNERLSTARVKRLDLSQPWSLCILKTEYTPTACLWQDGWVEWIHLPHISPKVITPYDIFCTQLIIKGRHRSKELFSKDP DYIVVPYTKVQFDLLLQEKEDWPISLLGFLGEVHFHLPKDPLLTFTLQTAIIFPHMTSTTPLEKGIVIFTDGSANGRSVTYIQGREPIIKENTQNTAQQAEIV AVITAFEEVSQPFNLYTDSKYVTGLFPEIETATLSPRTKIYTELKHLQRLIHKRQEKFYIGHIRGHTGLPGPLAQGNAYADSLTRILTA MMTVB_P03365_2mutB 8,085 WVQEISDSRPMLHIYLNGRRFLGLLNTGADKTCIAGRDWPANWPIHQTESSLQGLGMACGVARSSQPLRWQHEDKSGIIHPFVIPTLPFTLWGRDIMK DIKVRLMTDSPDDSQDLMIGAIESNLFADQISWKSDQPVWLNQWPLKQEKLQALQQLVTEQLQLGHLEESNSPWNTPVFVIKKKSGKWRLLQDLRAV NATMHDMGALQPGLPSPVAPPKGWEIIIIDLQDCFFNIKLHPEDCKRFAFSVPSPNFKRPYQRFQWKVLPQGMKNSPTLCQKFVDKAILTVRDKYQDS YIVHYMDDILLAHPSRSIVDEILTSMIQALNKHGLVVSTEKIQKYDNLKYLGTHIQGDSVSYQKLQIRTDKLRTLNDFQKLLGNINWIRPFLKLTTGELKPLF EILNPDSNPISTRKLTPEACKALQLMNERLSTARVKRLDLSQPWSLCILKTEYTPTACLWQDGVVEWIHLPHISPKVITPYDIFCTQLIIKGRHRSKELFSK DPDYIVVPYTKVQFDLLLQEKEDWPISLLGFLGEVHFHLPKDPLLTFTLQTAIIFPHMTSTTPLEKGIVIFTDGSANGRSVTYIQGREPIIKENTQNTAQQA EIVAVITAFEEVSQPFNLYTDSKYVTGLFPEIETATLSPRTKIYTELKHLQRLIHKRQEKFYIGHIRGHTGLPGPLAQGNAYADSLTRILT MMTVB_P03365_2mutB 8,086 WVQEISDSRPMLHIYLNGRRFLGLLNTGADKTCIAGRDWPANWPIHQTESSLQGLGMACGVARSSQPLRWQHEDKSGIIHPFVIPTLPFTLWGRDIMK DIKVRLMTDSPDDSQDLMIGAIESNLFADQISWKSDQPVWLNQWPLKQEKLQALQQLVTEQLQLGHLEESNSPWNTPVFVIKKKSGKWRLLQDLRAV NATMHDMGALQPGLPSPVAPPKGWEIIIIDLQDCFFNIKLHPEDCKRFAFSVPSPNFKRPYQRFQWKVLPQGMKNSPTLCQKFVDKAILTVRDKYQDS YIVHYMDDILLAHPSRSIVDEILTSMIQALNKHGLVVSTEKIQKYDNLKYLGTHIQGDSVSYQKLQIRTDKLRTLNDFQKLLGNINWIRPFLKLTTGELKPLF EILNPDSNPISTRKLTPEACKALQLMNERLSTARVKRLDLSQPWSLCILKTEYTPTACLWQDGVVEWIHLPHISPKVITPYDIFCTQLIIKGRHRSKELFSK DPDYIVVPYTKVQFDLLLQEKEDWPISLLGFLGEVHFHLPKDPLLTFTLQTAIIFPHMTSTTPLEKGIVIFTDGSANGRSVTYIQGREPIIKENTQNTAQQA EIVAVITAFEEVSQPFNLYTDSKYVTGLFPEIETATLSPRTKIYTELKHLQRLIHKRQEKFYIGHIRGHTGLPGPLAQGNAYADSLTRILT MMTVB_P03365_2mutBWS 8,087 VQEISDSRPMLHIYLNGRRFLGLLDTGADKTCIAGRDWPANWPIHQTESSLQGLGMACGVARSSQPLRWQHEDKSGIIHPFVIPTLPFTLWGRDIMKDI KVRLMTDSPDDSQDLMIGAIESNLFADQISWKSDQPVWLNQWPLKQEKLQALQQLVTEQLQLGHLEESNSPWNTPVFVIKKKSGKWRLLQDLRAVNA TMHDMGALQPGLPSPPAVPKGWEIIIIDLQDCFFNIKLHPEDCKRFAFSVPSPNFKRPYQRFQWKVLPQGMKNSPTLCQKFVDKAILTVRDKYQDSYIV HYMDDILLAHPSRSIVDEILTSMIQALNKHGLVVSTEKIQKYDNLKYLGTHIQGDSVSYQKLQIRTDKLRTLNDFQKLLGNINWIRPFLKLTTGELKPLFEIL NPDSNPISTRKLTPEACKALQLMNERLSTARVKRLDLSQPWSLCILKTEYTPTACLWQDGVVEWIHLPHISPKVITPYDIFCTQLIIKGRHRSKELFSKDP DYIVVPYTKVQFDLLLQEKEDWPISLLGFLGEVHFHLPKDPLLTFTLQTAIIFPHMTSTTPLEKGIVIFTDGSANGRSVTYIQGREPIIKENTQNTAQQAEIV AVITAFEEVSQPFNLYTDSKYVTGLFPEIETATLSPRTKIYTELKHLQRLIHKRQEKFYIGHIRGHTGLPGPLAQGNAYADSLTRILTA MMTVB_P03365_2mutBWS 8,088 VQEISDSRPMLHIYLNGRRFLGLLDTGADKTCIAGRDWPANWPIHQTESSLQGLGMACGVARSSQPLRWQHEDKSGIIHPFVIPTLPFTLWGRDIMKDI KVRLMTDSPDDSQDLMIGAIESNLFADQISWKSDQPVWLNQWPLKQEKLQALQQLVTEQLQLGHLEESNSPWNTPVFVIKKKSGKWRLLQDLRAVNA TMHDMGALQPGLPSPPAVPKGWEIIIIDLQDCFFNIKLHPEDCKRFAFSVPSPNFKRPYQRFQWKVLPQGMKNSPTLCQKFVDKAILTVRDKYQDSYIV HYMDDILLAHPSRSIVDEILTSMIQALNKHGLVVSTEKIQKYDNLKYLGTHIQGDSVSYQKLQIRTDKLRTLNDFQKLLGNINWIRPFLKLTTGELKPLFEIL NPDSNPISTRKLTPEACKALQLMNERLSTARVKRLDLSQPWSLCILKTEYTPTACLWQDGWVEWIHLPHISPKVITPYDIFCTQLIIKGRHRSKELFSKDP DYIVVPYTKVQFDLLLQEKEDWPISLLGFLGEVHFHLPKDPLLTFTLQTAIIFPHMTSTTPLEKGIVIFTDGSANGRSVTYIQGREPIIKENTQNTAQQAEIV AVITAFEEVSQPFNLYTDSKYVTGLFPEIETATLSPRTKIYTELKHLQRLIHKRQEKFYIGHIRGHTGLPGPLAQGNAYADSLTRILTA MMTVB_P03365_WS 8,089 VQEISDSRPMLHIYLNGRRFLGLLDTGADKTCIAGRDWPANWPIHQTESSLQGLGMACGVARSSQPLRWQHEDKSGIIHPFVIPTLPFTLWGRDIMKDI KVRLMTDSPDDSQDLMIGAIESNLFADQISWKSDQPVWLNQWPLKQEKLQALQQLVTEQLQLGHLEESNSPWNTPVFVIKKKSGKWRLLQDLRAVNA TMHDMGALQPGLPSPVAVPKGWEIIIIDLQDCFFNIKLHPEDCKRFAFSVPSPNFKRPYQRFQWKVLPQGMKNSPTLCQKFVDKAILTVRDKYQDSYIV HYMDDILLAHPSRSIVDEILTSMIQALNKHGLVVSTEKIQKYDNLKYLGTHIQGDSVSYQKLQIRTDKLRTLNDFQKLLGNINWIRPFLKLTTGELKPLFEIL NGDSNPISTRKLTPEACKALQLMNERLSTARVKRLDLSQPWSLCILKTEYTPTACLWQDGVVEWIHLPHISPKVITPYDIFCTQLIIKGRHRSKELFSKDP DYIVVPYTKVQFDLLLQEKEDWPISLLGFLGEVHFHLPKDPLLTFTLQTAIIFPHMTSTTPLEKGIVIFTDGSANGRSVTYIQGREPIIKENTQNTAQQAEIV AVITAFEEVSQPFNLYTDSKYVTGLFPEIETATLSPRTKIYTELKHLQRLIHKRQEKFYIGHIRGHTGLPGPLAQGNAYADSLTRILTA MMTVB_P03365_WS 8,090 VQEISDSRPMLHIYLNGRRFLGLLDTGADKTCIAGRDWPANWPIHQTESSLQGLGMACGVARSSQPLRWQHEDKSGIIHPFVIPTLPFTLWGRDIMKDI KVRLMTDSPDDSQDLMIGAIESNLFADQISWKSDQPVWLNQWPLKQEKLQALQQLVTEQLQLGHLEESNSPWNTPVFVIKKKSGKWRLLQDLRAVNA TMHDMGALQPGLPSPVAVPKGWEIIIIDLQDCFFNIKLHPEDCKRFAFSVPSPNFKRPYQRFQWKVLPQGMKNSPTLCQKFVDKAILTVRDKYQDSYIV HYMDDILLAHPSRSIVDEILTSMIQALNKHGLVVSTEKIQKYDNLKYLGTHIQGDSVSYQKLQIRTDKLRTLNDFQKLLGNINWIRPFLKLTTGELKPLFEIL NGDSNPISTRKLTPEACKALQLMNERLSTARVKRLDLSQPWSLCILKTEYTPTACLWQDGVVEWIHLPHISPKVITPYDIFCTQLIIKGRHRSKELFSKDP DYIVVPYTKVQFDLLLQEKEDWPISLLGFLGEVHFHLPKDPLLTFTLQTAIIFPHMTSTTPLEKGIVIFTDGSANGRSVTYIQGREPIIKENTQNTAQQAEIV AVITAFEEVSQPFNLYTDSKYVTGLFPEIETATLSPRTKIYTELKHLQRLIHKRQEKFYIGHIRGHTGLPGPLAQGNAYADSLTRILTA MMTVB_P03365-Pro 8,091 GRDIMKDIKVRLMTDSPDDSQDLMIGAIESNLFADQISWKSDQPVWLNQWPLKQEKLQALQQLVTEQLQLGHLEESNSPWNTPVFVIKKKSGKWRLL QDLRAVNATMHDMGALQPGLPSPVAVPKGWEIIIIDLQDCFFNIKLHPEDCKRFAFSVPSPNFKRPYQRFQWKVLPQGMKNSPTLCQKFVDKAILTVR DKYQDSYIVHYMDDILLAHPSRSIVDEILTSMIQALNKHGLVVSTEKIQKYDNLKYLGTHIQGDSVSYQKLQIRTDKLRTLNDFQKLLGNINWIRPFLKLTT GELKPLFEILNGDSNPISTRKLTPEACKALQLMNERLSTARVKRLDLSQPWSLCILKTEYTPTACLWQDGVVEWIHLPHISPKVITPYDIFCTQLIIKGRHR SKELFSKDPDYIVVPYTKVQFDLLLQEKEDWPISLLGFLGEVHFHLPKDPLLTFTLQTAIIFPHMTSTTPLEKGIVIFTDGSANGRSVTYIQGREPIIKENTQ NTAQQAEIVAVITAFEEVSQPFNLYTDSKYVTGLFPEIETATLSPRTKIYTELKHLQRLIHKRQEKFYIGHIRGHTGLPGPLAQGNAYADSLTRILT MMTVB_P03365-Pro 8,092 GRDIMKDIKVRLMTDSPDDSQDLMIGAIESNLFADQISWKSDQPVWLNQWPLKQEKLQALQQLVTEQLQLGHLEESNSPWNTPVFVIKKKSGKWRLL QDLRAVNATMHDMGALQPGLPSPVAVPKGWEIIIIDLQDCFFNIKLHPEDCKRFAFSVPSPNFKRPYQRFQWKVLPQGMKNSPTLCQKFVDKAILTVR DKYQDSYIVHYMDDILLAHPSRSIVDEILTSMIQALNKHGLVVSTEKIQKYDNLKYLGTHIQGDSVSYQKLQIRTDKLRTLNDFQKLLGNINWIRPFLKLTT GELKPLFEILNGDSNPISTRKLTPEACKALQLMNERLSTARVKRLDLSQPWSLCILKTEYTPTACLWQDGVVEWIHLPHISPKVITPYDIFCTQLIIKGRHR SKELFSKDPDYIVVPYTKVQFDLLLQEKEDWPISLLGFLGEVHFHLPKDPLLTFTLQTAIIFPHMTSTTPLEKGIVIFTDGSANGRSVTYIQGREPIIKENTQ NTAQQAEIVAVITAFEEVSQPFNLYTDSKYVTGLFPEIETATLSPRTKIYTELKHLQRLIHKRQEKFYIGHIRGHTGLPGPLAQGNAYADSLTRILT MMTVB_P03365-Pro_2mut 8,093 GRDIMKDIKVRLMTDSPDDSQDLMIGAIESNLFADQISWKSDQPVWLNQWPLKQEKLQALQQLVTEQLQLGHLEESNSPWNTPVFVIKKKSGKWRLL QDLRAVNATMHDMGALQPGLPSPVAVPKGWEIIIIDLQDCFFNIKLHPEDCKRFAFSVPSPNFKRPYQRFQWKVLPQGMKNSPTLCQKFVDKAILTVR DKYQDSYIVHYMDDILLAHPSRSIVDEILTSMIQALNKHGLVVSTEKIQKYDNLKYLGTHIQGDSVSYQKLQIRTDKLRTLNDFQKLLGNINWIRPFLKLTT GELKPLFEILNPDSNPISTRKLTPEACKALQLMNERLSTARVKRLDLSQPWSLCILKTEYTPTACLWQDGVVEWIHLPHISPKVITPYDIFCTQLIIKGRHR SKELFSKDPDYIVVPYTKVQFDLLLQEKEDWPISLLGFLGEVHFHLPKDPLLTFTLQTAIIFPHMTSTTPLEKGIVIFTDGSANGRSVTYIQGREPIIKENTQ NTAQQAEIVAVITAFEEVSQPFNLYTDSKYVTGLFPEIETATLSPRTKIYTELKHLQRLIHKRQEKFYIGHIRGHTGLPGPLAQGNAYADSLTRILT MMTVB_P03365-Pro_2mut 8,094 GRDIMKDIKVRLMTDSPDDSQDLMIGAIESNLFADQISWKSDQPVWLNQWPLKQEKLQALQQLVTEQLQLGHLEESNSPWNTPVFVIKKKSGKWRLL QDLRAVNATMHDMGALQPGLPSPVAVPKGWEIIIIDLQDCFFNIKLHPEDCKRFAFSVPSPNFKRPYQRFQWKVLPQGMKNSPTLCQKFVDKAILTVR DKYQDSYIVHYMDDILLAHPSRSIVDEILTSMIQALNKHGLVVSTEKIQKYDNLKYLGTHIQGDSVSYQKLQIRTDKLRTLNDFQKLLGNINWIRPFLKLTT GELKPLFEILNPDSNPISTRKLTPEACKALQLMNERLSTARVKRLDLSQPWSLCILKTEYTPTACLWQDGVVEWIHLPHISPKVITPYDIFCTQLIIKGRHR SKELFSKDPDYIVVPYTKVQFDLLLQEKEDWPISLLGFLGEVHFHLPKDPLLTFTLQTAIIFPHMTSTTPLEKGIVIFTDGSANGRSVTYIQGREPIIKENTQ NTAQQAEIVAVITAFEEVSQPFNLYTDSKYVTGLFPEIETATLSPRTKIYTELKHLQRLIHKRQEKFYIGHIRGHTGLPGPLAQGNAYADSLTRILT MMTVB_P03365-Pro_2mutB 8,095 GRDIMKDIKVRLMTDSPDDSQDLMIGAIESNLFADQISWKSDQPVWLNQWPLKQEKLQALQQLVTEQLQLGHLEESNSPWNTPVFVIKKKSGKWRLL QDLRAVNATMHDMGALQPGLPSPVAPPKGWEIIIIDLQDCFFNIKLHPEDCKRFAFSVPSPNFKRPYQRFQWKVLPQGMKNSPTLCQKFVDKAILTVR DKYQDSYIVHYMDDILLAHPSRSIVDEILTSMIQALNKHGLVVSTEKIQKYDNLKYLGTHIQGDSVSYQKLQIRTDKLRTLNDFQKLLGNINWIRPFLKLTT GELKPLFEILNPDSNPISTRKLTPEACKALQLMNERLSTARVKRLDLSQPWSLCILKTEYTPTACLWQDGVVEWIHLPHISPKVITPYDIFCTQLIIKGRHR SKELFSKDPDYIVVPYTKVQFDLLLQEKEDWPISLLGFLGEVHFHLPKDPLLTFTLQTAIIFPHMTSTTPLEKGIVIFTDGSANGRSVTYIQGREPIIKENTQ NTAQQAEIVAVITAFEEVSQPFNLYTDSKYVTGLFPEIETATLSPRTKIYTELKHLQRLIHKRQEKFYIGHIRGHTGLPGPLAQGNAYADSLTRILT MMTVB_P03365-Pro_2mutB 8,096 GRDIMKDIKVRLMTDSPDDSQDLMIGAIESNLFADQISWKSDQPVWLNQWPLKQEKLQALQQLVTEQLQLGHLEESNSPWNTPVFVIKKKSGKWRLL QDLRAVNATMHDMGALQPGLPSPVAPPKGWEIIIIDLQDCFFNIKLHPEDCKRFAFSVPSPNFKRPYQRFQWKVLPQGMKNSPTLCQKFVDKAILTVR DKYQDSYIVHYMDDILLAHPSRSIVDEILTSMIQALNKHGLVVSTEKIQKYDNLKYLGTHIQGDSVSYQKLQIRTDKLRTLNDFQKLLGNINWIRPFLKLTT GELKPLFEILNPDSNPISTRKLTPEACKALQLMNERLSTARVKRLDLSQPWSLCILKTEYTPTACLWQDGVVEWIHLPHISPKVITPYDIFCTQLIIKGRHR SKELFSKDPDYIVVPYTKVQFDLLLQEKEDWPISLLGFLGEVHFHLPKDPLLTFTLQTAIIFPHMTSTTPLEKGIVIFTDGSANGRSVTYIQGREPIIKENTQ NTAQQAEIVAVITAFEEVSQPFNLYTDSKYVTGLFPEIETATLSPRTKIYTELKHLQRLIHKRQEKFYIGHIRGHTGLPGPLAQGNAYADSLTRILT MPMV_P07572 8,097 LTAAIDILAPQQCAEPITWKSDEPVWVDQWPLTNDKLAAAQQLVQEQLEAGHITESSSPWNTPIFVIKKKSGKWRLLQDLRAVNATMVLMGALQPGLP SPVAIPQGYLKIIIDLKDCFFSIPLHPSDQKRFAFSLPSTNFKEPMQRFQWKVLPQGMANSPTLCQKYVATAIHKVRHAWKQMYIIHYMDDILIAGKDGQ QVLQCFDQLKQELTAAGLHIAPEKVQLQDPYTYLGFELNGPKITNQKAVIRKDKLQTLNDFQKLLGDINWLRPYLKLTTGDLKPLFDTLKGDSDPNSHR SLSKEALASLEKVETAIAEQFVTHINYSLPLIFLIFNTALTPTGLFWQDNPIMWIHLPASPKKVLLPYYDAIADLIILGRDHSKKYFGIEPSTIIQPYSKSQIDW LMQNTEMWPIACASFVGILDNHYPPNKLIQFCKLHTFVFPQIISKTPLNNALLVFTDGSSTGMAAYTLTDTTIKFQTNLNSAQLVELQALIAVLSAFPNQPL NIYTDSAYLAHSIPLLETVAQIKHISETAKLFLQCQQLIYNRSIPFYIGHVRAHSGLPGPIAQGNQRADLATKIVASNINT MPMV_P07572_2mutB 8,098 LTAAIDILAPQQCAEPITWKSDEPVWVDQWPLTNDKLAAAQQLVQEQLEAGHITESSSPWNTPIFVIKKKSGKWRLLQDLRAVNATMVLMGALQPGLP SPVAPPQGYLKIIIDLKDCFFSIPLHPSDQKRFAFSLPSTNFKEPMQRFQWKVLPQGMANSPTLCQKYVATAIHKVRHAWKQMYIIHYMDDILIAGKDGQ QVLQCFDQLKQELTAAGLHIAPEKVQLQDPYTYLGFELNGPKITNQKAVIRKDKLQTLNDFQKLLGDINWLRPYLKLTTGDLKPLFDTLKPDSDPNSHRS LSKEALASLEKVETAIAEQFVTHINYSLPLIFLIFNTALTPTGLFWQDNPIMWIHLPASPKKVLLPYYDAIADLIILGRDHSKKYFGIEPSTIIQPYSKSQIDWL MQNTEMWPIACASFVGILDNHYPPNKLIQFCKLHTFVFPQIISKTPLNNALLVFTDGSSTGMAAYTLTDTTIKFQTNLNSAQLVELQALIAVLSAFPNQPL NIYTDSAYLAHSIPLLETVAQIKHISETAKLFLQCQQLIYNRSIPFYIGHVRAHSGLPGPIAQGNQRADLATKIVASNINT PERV_Q4VFZ2 8,099 TLQLDDEYRLYSPLVKPDQNIQFWLEQFPQAWAETAGMGLAKQVPPQVIQLKASATPVSVRQYPLSKEAQEGIRPHVQRLIQQGILVPVQSPWNTPLL PVRKPGTNDYRPVQDLREVNKRVQDIHPTVPNPYNLLCALPPQRSWYTVLDLKDAFFCLRLHPTSQPLFAFEWRDPGTGRTGQLTWTRLPQGFKNS PTIFDEALHRDLANFRIQHPQVTLLQYVDDLLLAGATKQDCLEGTKALLLELSDLGYRASAKKAQICRREVTYLGYSLRDGQRWLTEARKKTVVQIPAPT TAKQVREFLGTAGFCRLWIPGFATLAAPLYPLTKEKGEFSWAPEHQKAFDAIKKALLSAPALALPDVTKPFTLYVDERKGVARGVLTQTLGPWRRPVA YLSKKLDPVASGWPVCLKAIAAVAILVKDADKLTLGQNITVIAPHALENIVRQPPDRWMTNARMTHYQSLLLTERVTFAPPAALNPATLLPEETDEPVTH DCHQLLIEETGVRKDLTDIPLTGEVLTWFTDGSSYVVEGKRMAGAAVVDGTRTIWASSLPEGTSAQKAELMALTQALRLAEGKSINIYTDSRYAFATAH VHGAIYKQRGLLTSAGREIKNKEEILSLLEALHLPKRLAIIHCPGHQKAKDPISRGNQMADRVAKQAAQGVNLL PERV_Q4VFZ2 8,100 TLQLDDEYRLYSPLVKPDQNIQFWLEQFPQAWAETAGMGLAKQVPPQVIQLKASATPVSVRQYPLSKEAQEGIRPHVQRLIQQGILVPVQSPWNTPLL PVRKPGTNDYRPVQDLREVNKRVQDIHPTVPNPYNLLCALPPQRSWYTVLDLKDAFFCLRLHPTSQPLFAFEWRDPGTGRTGQLTWTRLPQGFKNS PTIFDEALHRDLANFRIQHPQVTLLQYVDDLLLAGATKQDCLEGTKALLLELSDLGYRASAKKAQICRREVTYLGYSLRDGQRWLTEARKKTVVQIPAPT TAKQVREFLGTAGFCRLWIPGFATLAAPLYPLTKEKGEFSWAPEHQKAFDAIKKALLSAPALALPDVTKPFTLYVDERKGVARGVLTQTLGPWRRPVA YLSKKLDPVASGWPVCLKAIAAVAILVKDADKLTLGQNITVIAPHALENIVRQPPDRWMTNARMTHYQSLLLTERVTFAPPAALNPATLLPEETDEPVTH DCHQLLIEETGVRKDLTDIPLTGEVLTWFTDGSSYVVEGKRMAGAAVVDGTRTIWASSLPEGTSAQKAELMALTQALRLAEGKSINIYTDSRYAFATAH VHGAIYKQRGLLTSAGREIKNKEEILSLLEALHLPKRLAIIHCPGHQKAKDPISRGNQMADRVAKQAAQGVNLL PERV_Q4VFZ2_3mut 8,101 TLQLDDEYRLYSPLVKPDQNIQFWLEQFPQAWAETAGMGLAKQVPPQVIQLKASATPVSVRQYPLSKEAQEGIRPHVQRLIQQGILVPVQSPWNTPLL PVRKPGTNDYRPVQDLREVNKRVQDIHPTVPNPYNLLCALPPQRSWYTVLDLKDAFFCLRLHPTSQPLFAFEWRDPGTGRTGQLTWTRLPQGFKNS PTIFNEALHRDLANFRIQHPQVTLLQYVDDLLLAGATKQDCLEGTKALLLELSDLGYRASAKKAQICRREVTYLGYSLRDGQRWLTEARKKTVVQIPAPT TAKQVREFLGTAGFCRLWIPGFATLAAPLYPLTKPKGEFSWAPEHQKAFDAIKKALLSAPALALPDVTKPFTLYVDERKGVARGVLTQTLGPWRRPVA YLSKKLDPVASGWPVCLKAIAAVAILVKDADKLTLGQNITVIAPHALENIVRQPPDRWMTNARMTHYQSLLLTERVTFAPPAALNPATLLPEETDEPVTH DCHQLLIEETGVRKDLTDIPLTGEVLTWFTDGSSYVVEGKRMAGAAVVDGTRTIWASSLPEGTSAQKAELMALTQALRLAEGKSINIYTDSRYAFATAH VHGAIYKQRGWLTSAGREIKNKEEILSLLEALHLPKRLAIIHCPGHQKAKDPISRGNQMADRVAKQAAQGVNLL PERV_Q4VFZ2_3mut 8,102 TLQLDDEYRLYSPLVKPDQNIQFWLEQFPQAWAETAGMGLAKQVPPQVIQLKASATPVSVRQYPLSKEAQEGIRPHVQRLIQQGILVPVQSPWNTPLL PVRKPGTNDYRPVQDLREVNKRVQDIHPTVPNPYNLLCALPPQRSWYTVLDLKDAFFCLRLHPTSQPLFAFEWRDPGTGRTGQLTWTRLPQGFKNS PTIFNEALHRDLANFRIQHPQVTLLQYVDDLLLAGATKQDCLEGTKALLLELSDLGYRASAKKAQICRREVTYLGYSLRDGQRWLTEARKKTVVQIPAPT TAKQVREFLGTAGFCRLWIPGFATLAAPLYPLTKPKGEFSWAPEHQKAFDAIKKALLSAPALALPDVTKPFTLYVDERKGVARGVLTQTLGPWRRPVA YLSKKLDPVASGWPVCLKAIAAVAILVKDADKLTLGQNITVIAPHALENIVRQPPDRWMTNARMTHYQSLLLTERVTFAPPAALNPATLLPEETDEPVTH DCHQLLIEETGVRKDLTDIPLTGEVLTWFTDGSSYVVEGKRMAGAAVVDGTRTIWASSLPEGTSAQKAELMALTQALRLAEGKSINIYTDSRYAFATAH VHGAIYKQRGWLTSAGREIKNKEEILSLLEALHLPKRLAIIHCPGHQKAKDPISRGNQMADRVAKQAAQGVNLL PERV_Q4VFZ2_3mutA_WS 8,103 LDDEYRLYSPLVKPDQNIQFWLEQFPQAWAETAGMGLAKQVPPQVIQLKASATPVSVRQYPLSKEAQEGIRPHVQRLIQQGILVPVQSPWNTPLLPVR KPGTNDYRPVQDLREVNKRVQDIHPTVPNPYNLLCALPPQRSWYTVLDLKDAFFCLRLHPTSQPLFAFEWRDPGTGRTGQLTWTRLPQGFKNSPTIF NEALHRDLANFRIQHPQVTLLQYVDDLLLAGATKQDCLEGTKALLLELSDLGYRASAKKAQICRREVTYLGYSLRDGQRWLTEARKKTVQIPAPTTAK QVREFLGKAGFCRLFIPGFATLAAPLYPLTKPKGEFSWAPEHQKAFDAIKKALLSAPALALPDVTKPFTLYVDERKGVARGVLTQTLGPWRRPVAYLSK KLDPVASGWPVCLKAIAAVAILVKDADKLTLGQNITVIAPHALENIVRQPPDRWMTNARMTHYQSLLLTERVTFAPPAALNPATLLPEETDEPVTHDCHQ LLIEETGVRKDLTDIPLTGEVLTWFTDGSSYVVEGKRMAGAAVVDGTRTIWASSLPEGTSAQKAELMALTQALRLAEGKSINIYTDSRYAFATAHVHGAI YKQRGWLTSAGREIKNKEEILSLLEALHLPKRLAIIHCPGHQKAKDPISRGNQMADRVAKQAAQGVNLLP PERV_Q4VFZ2_3mutA_WS 8,104 LDDEYRLYSPLVKPDQNIQFWLEQFPQAWAETAGMGLAKQVPPQVIQLKASATPVSVRQYPLSKEAQEGIRPHVQRLIQQGILVPVQSPWNTPLLPVR KPGTNDYRPVQDLREVNKRVQDIHPTVPNPYNLLCALPPQRSWYTVLDLKDAFFCLRLHPTSQPLFAFEWRDPGTGRTGQLTWTRLPQGFKNSPTIF NEALHRDLANFRIQHPQVTLLQYVDDLLLAGATKQDCLEGTKALLLELSDLGYRASAKKAQICRREVTYLGYSLRDGQRWLTEARKKTVVQIPAPTTAK QVREFLGKAGFCRLFIPGFATLAAPLYPLTKPKGEFSWAPEHQKAFDAIKKALLSAPALALPDVTKPFTLYVDERKGVARGVLTQTLGPWRRPVAYLSK KLDPVASGWPVCLKAIAAVAILVKDADKLTLGQNITVIAPHALENIVRQPPDRWMTNARMTHYQSLLLTERVTFAPPAALNPATLLPEETDEPVTHDCHQ LLIEETGVRKDLTDIPLTGEVLTWFTDGSSYVVEGKRMAGAAVVDGTRTIWASSLPEGTSAQKAELMALTQALRLAEGKSINIYTDSRYAFATAHVHGAI YKQRGWLTSAGREIKNKEEILSLLEALHLPKRLAIIHCPGHQKAKDPISRGNQMADRVAKQAAQGVNLLP SFV1_P23074 8,105 MDPLQLLQPLEAEIKGTKLKAHWNSGATITCVPEAFLEDERPIQTMLIKTIHGEKQQDVYYLTFKVQGRKVEAEVLASPYDYILLNPSDVPWLMKKPLQL TVLVPLHEYQERLLQQTALPKEQKELLQKLFLKYDALWQHWENQVGHRRIKPHNIATGTLAPRPQKQYPINPKAKPSIQIVIDDLLKQGVLIQQNSTMNT PVYPVPKPDGKWRMVLDYREVNKTIPLIAAQNQHSAGILSSIYRGKYKTTLDLTNGFWAHPITPESYWLTAFTWQGKQYCWTRLPQGFLNSPALFTAD WDLLKEIPNVQAYVDDIYISHDDPQEHLEQLEKIFSILLNAGYVVSLKKSEIAQREVEFLGFNITKEGRGLTDTFKQKLLNITPPKDLKQLQSILGLLNFAR NFIPNYSELVKPLYTIVANANGKFISWTEDNSNQLQHIISVLNQADNLEERNPETRLIIKVNSSPSAGYIRYYNEGSKRPIMYVNYIFSKAEAKFTQTEKLL TTMHKGLIKAMDLAMGQEILVYSPIVSMTKIQRTPLPERKALPVRWITWMTYLEDPRIQFHYDKSLPELQQIPNVTEDVIAKTKHPSEFAMVFYTDGSAIK HPDVNKSHSAGMGIAQVQFIPEYKIVHQWSIPLGDHTAQLAEIAAVEFACKKALKISGPVLIVTDSFYVAESANKELPYWKSNGFLNNKKKPLRHVSKW KSIAECLQLKPDIIIMHEKGHQQPMTTLHTEGNNLADKLATQGSYVVH SFV1_P23074_2mut 8,106 MDPLQLLQPLEAEIKGTKLKAHWNSGATITCVPEAFLEDERPIQTMLIKTIHGEKQQDVYYLTFKVQGRKVEAEVLASPYDYILLNPSDVPWLMKKPLQL TVLVPLHEYQERLLQQTALPKEQKELLQKLFLKYDALWQHWENQVGHRRIKPHNIATGTLAPRPQKQYPINPKAKPSIQIVIDDLLKQGVLIQQNSTMNT PVYPVPKPDGKWRMVLDYREVNKTIPLIAAQNQHSAGILSSIYRGKYKTTLDLTNGFWAHPITPESYWLTAFTWQGKQYCWTRLPQGFLNSPALFNAD WVDLLKEIPNVQAYVDDIYISHDDPQEHLEQLEKIFSILLNAGYVVSLKKSEIAQREVEFLGFNITKEGRGLTDTFKQKLLNITPPKDLKQLQSILGLLNFAR NFIPNYSELVKPLYTIVAPANGKFISWTEDNSNQLQHIISVLNQADNLEERNPETRLIIKVNSSPSAGYIRYYNEGSKRPIMYVNYIFSKAEAKFTQTEKLLT TMHKGLIKAMDLAMGQEILVYSPIVSMTKIQRTPLPERKALPVRWITWMTYLEDPRIQFHYDKSLPELQQIPNVTEDVIAKTKHPSEFAMVFYTDGSAIKH PDVNKSHSAGMGIAQVQFIPEYKIVHQWSIPLGDHTAQLAEIAAVEFACKKALKISGPVLIVTDSFYVAESANKELPYWKSNGFLNNKKKPLRHVSKWK SIAECLQLKPDIIIMHEKGHQQPMTTLHTEGNNLADKLATQGSYVVH SFV1_P23074_2mutA 8,107 MDPLQLLQPLEAEIKGTKLKAHWNSGATITCVPEAFLEDERPIQTMLIKTIHGEKQQDVYYLTFKVQGRKVEAEVLASPYDYILLNPSDVPWLMKKPLQL TVLVPLHEYQERLLQQTALPKEQKELLQKLFLKYDALWQHWENQVGHRRIKPHNIATGTLAPRPQKQYPINPKAKPSIQIVIDDLLKQGVLIQQNSTMNT PVYPVPKPDGKWRMVLDYREVNKTIPLIAAQNQHSAGILSSIYRGKYKTTLDLTNGFWAHPITPESYWLTAFTWQGKQYCWTRLPQGFLNSPALFNAD WVDLLKEIPNVQAYVDDIYISHDDPQEHLEQLEKIFSILLNAGYVVSLKKSEIAQREVEFLGFNITKEGRGLTDTFKQKLLNITPPKDLKQLQSILGKLNFAR NFIPNYSELVKPLYTIVAPANGKFISWTEDNSNQLQHIISVLNQADNLEERNPETRLIIKVNSSPSAGYIRYYNEGSKRPIMYVNYIFSKAEAKFTQTEKLLT TMHKGLIKAMDLAMGQEILVYSPIVSMTKIQRTPLPERKALPVRWITWMTYLEDPRIQFHYDKSLPELQQIPNVTEDVIAKTKHPSEFAMVFYTDGSAIKH PDVNKSHSAGMGIAQVQFIPEYKIVHQWSIPLGDHTAQLAEIAAVEFACKKALKISGPVLIVTDSFYVAESANKELPYWKSNGFLNNKKKPLRHVSKWK SIAECLQLKPDIIIMHEKGHQQPMTTLHTEGNNLADKLATQGSYVVH SFV1_P23074-Pro 8,108 VPWLMKKPLQLTVLVPLHEYQERLLQQTALPKEQKELLQKLFLKYDALWQHWENQVGHRRIKPHNIATGTLAPRPQKQYPINPKAKPSIQIVIDDLLKQ GVLIQQNSTMNTPVYPVPKPDGKWRMVLDYREVNKTIPLIAAQNQHSAGILSSIYRGKYKTTLDLTNGFWAHPITPESYWLTAFTWQGKQYCWTRLPQ GFLNSPALFTADVVDLLKEIPNVQAYVDDIYISHDDPQEHLEQLEKIFSILLNAGYVVSLKKSEIAQREVEFLGFNITKEGRGLTDTFKQKLLNITPPKDLKQ LQSILGLLNFARNFIPNYSELVKPLYTIVANANGKFISWTEDNSNQLQHIISVLNQADNLEERNPETRLIIKVNSSPSAGYIRYYNEGSKRPIMYVNYIFSKA EAKFTQTEKLLTTMHKGLIKAMDLAMGQEILVYSPIVSMTKIQRTPLPERKALPVRWITWMTYLEDPRIQFHYDKSLPELQQIPNVTEDVIAKTKHPSEFA MVFYTDGSAIKHPDVNKSHSAGMGIAQVQFIPEYKIVHQWSIPLGDHTAQLAEIAAVEFACKKALKISGPVLIVTDSFYVAESANKELPYWKSNGFLNNK KKPLRHVSKWKSIAECLQLKPDIIIMHEKGHQQPMTTLHTEGNNLADKLATQGSYVVH SFV1_P23074Pro_2mut 8,109 VPWLMKKPLQLTVLVPLHEYQERLLQQTALPKEQKELLQKLFLKYDALWQHWENQVGHRRIKPHNIATGTLAPRPQKQYPINPKAKPSIQIVIDDLLKQ GVLIQQNSTMNTPVYPVPKPDGKWRMVLDYREVNKTIPLIAAQNQHSAGILSSIYRGKYKTTLDLTNGFWAHPITPESYWLTAFTWQGKQYCWTRLPQ GFLNSPALFNADVVDLLKEIPNVQAYVDDIYISHDDPQEHLEQLEKIFSILLNAGYVVSLKKSEIAQREVEFLGFNITKEGRGLTDTFKQKLLNITPPKDLK QLQSILGLLNFARNFIPNYSELVKPLYTIVAPANGKFISWTEDNSNQLQHIISVLNQADNLEERNPETRLIIKVNSSPSAGYIRYYNEGSKRPIMYVNYIFSK AEAKFTQTEKLLTTMHKGLIKAMDLAMGQEILVYSPIVSMTKIQRTPLPERKALPVRWITWMTYLEDPRIQFHYDKSLPELQQIPNVTEDVIAKTKHPSEF AMVFYTDGSAIKHPDVNKSHSAGMGIAQVQFIPEYKIVHQWSIPLGDHTAQLAEIAAVEFACKKALKISGPVLIVTDSFYVAESANKELPYWKSNGFLNN KKKPLRHVSKWKSIAECLQLKPDIIIMHEKGHQQPMTTLHTEGNNLADKLATQGSYVVH SFV1_P23074-Pro_2mutA 8,110 VPWLMKKPLQLTVLVPLHEYQERLLQQTALPKEQKELLQKLFLKYDALWQHWENQVGHRRIKPHNIATGTLAPRPQKQYPINPKAKPSIQIVIDDLLKQ GVLIQQNSTMNTPVYPVPKPDGKWRMVLDYREVNKTIPLIAAQNQHSAGILSSIYRGKYKTTLDLTNGFWAHPITPESYWLTAFTWQGKQYCWTRLPQ GFLNSPALFNADVVDLLKEIPNVQAYVDDIYISHDDPQEHLEQLEKIFSILLNAGYVVSLKKSEIAQREVEFLGFNITKEGRGLTDTFKQKLLNITPPKDLK QLQSILGKLNFARNFIPNYSELVKPLYTIVAPANGKFISWTEDNSNQLQHIISVLNQADNLEERNPETRLIIKVNSSPSAGYIRYYNEGSKRPIMYVNYIFSK AEAKFTQTEKLLTTMHKGLIKAMDLAMGQEILVYSPIVSMTKIQRTPLPERKALPVRWITWMTYLEDPRIQFHYDKSLPELQQIPNVTEDVIAKTKHPSEF AMVFYTDGSAIKHPDVNKSHSAGMGIAQVQFIPEYKIVHQWSIPLGDHTAQLAEIAAVEFACKKALKISGPVLIVTDSFYVAESANKELPYWKSNGFLNN KKKPLRHVSKWKSIAECLQLKPDIIIMHEKGHQQPMTTLHTEGNNLADKLATQGSYVVH SFV3L_P27401 8,111 MDPLQLLQPLEAEIKGTKLKAHWNSGATITCVPQAFLEEEVPIKNIWIKTIHGEKEQPVYYLTFKIQGRKVEAEVISSPYDYILVSPSDIPWLMKKPLQLTT LVPLQEYEERLLKQTMLTGSYKEKLQSLFLKYDALWQHWENQVGHRRIKPHHIATGTVNPRPQKQYPINPKAKASIQTVINDLLKQGVLIQQNSIMNTP VYPVPKPDGKWRMVLDYREVNKTIPLIAAQNQHSAGILSSIFRGKYKTTLDLSNGFWAHSITPESYWLTAFTWLGQQYCWTRLPQGFLNSPALFTADV VDLLKEVPNVQVYVDDIYISHDDPREHLEQLEKVFSLLLNAGYVVSLKKSEIAQHEVEFLGFNITKEGRGLTETFKQKLLNITPPRDLKQLQSILGLLNFAR NFIPNFSELVKPLYNIIATANGKYITWTTDNSQQLQNIISMLNSAENLEERNPEVRLIMKVNTSPSAGYIRFYNEFAKRPIMYLNYVYTKAEVKFTNTEKLL TTIHKGLIKALDLGMGQEILVYSPIVSMTKIQKTPLPERKALPIRWITWMSYLEDPRIQFHYDKTLPELQQVPTVTDDIIAKIKHPSEFSMVFYTDGSAIKHP NVNKSHNAGMGIAQVQFKPEFTVINTWSIPLGDHTAQLAEVAAVEFACKKALKIDGPVLIVTDSFYVAESVNKELPYWQSNGFFNNKKKPLKHVSKWK SIADCIQLKPDIIIIHEKGHQPTASTFHTEGNNLADKLATQGSYVVN SFV3L_P27401_2mut 8,112 MDPLQLLQPLEAEIKGTKLKAHWNSGATITCVPQAFLEEEVPIKNIWIKTIHGEKEQPVYYLTFKIQGRKVEAEVISSPYDYILVSPSDIPWLMKKPLQLTT LVPLQEYEERLLKQTMLTGSYKEKLQSLFLKYDALWQHWENQVGHRRIKPHHIATGTVNPRPQKQYPINPKAKASIQTVINDLLKQGVLIQQNSIMNTP VYPVPKPDGKWRMVLDYREVNKTIPLIAAQNQHSAGILSSIFRGKYKTTLDLSNGFWAHSITPESYWLTAFTWLGQQYCWTRLPQGFLNSPALFNADV VDLLKEVPNVQVYVDDIYISHDDPREHLEQLEKVFSLLLNAGYVVSLKKSEIAQHEVEFLGFNITKEGRGLTETFKQKLLNITPPRDLKQLQSILGLLNFAR NFIPNFSELVKPLYNIIATAPGKYITWTTDNSQQLQNIISMLNSAENLEERNPEVRLIMKVNTSPSAGYIRFYNEFAKRPIMYLNYVYTKAEVKFTNTEKLL TTIHKGLIKALDLGMGQEILVYSPIVSMTKIQKTPLPERKALPIRWITWMSYLEDPRIQFHYDKTLPELQQVPTVTDDIIAKIKHPSEFSMVFYTDGSAIKHP NVNKSHNAGMGIAQVQFKPEFTVINTWSIPLGDHTAQLAEVAAVEFACKKALKIDGPVLIVTDSFYVAESVNKELPYWQSNGFFNNKKKPLKHVSKWK SIADCIQLKPDIIIIHEKGHQPTASTFHTEGNNLADKLATQGSYVVN SFV3L_P27401_2mutA 8,113 MDPLQLLQPLEAEIKGTKLKAHWNSGATITCVPQAFLEEEVPIKNIWIKTIHGEKEQPVYYLTFKIQGRKVEAEVISSPYDYILVSPSDIPWLMKKPLQLTT LVPLQEYEERLLKQTMLTGSYKEKLQSLFLKYDALWQHWENQVGHRRIKPHHIATGTVNPRPQKQYPINPKAKASIQTVINDLLKQGVLIQQNSIMNTP VYPVPKPDGKWRMVLDYREVNKTIPLIAAQNQHSAGILSSIFRGKYKTTLDLSNGFWAHSITPESYWLTAFTWLGQQYCWTRLPQGFLNSPALFNADV VDLLKEVPNVQVYVDDIYISHDDPREHLEQLEKVFSLLLNAGYVVSLKKSEIAQHEVEFLGFNITKEGRGLTETFKQKLLNITPPRDLKQLQSILGKLNFA RNFIPNFSELVKPLYNIIATAPGKYITWTTDNSQQLQNIISMLNSAENLEERNPEVRLIMKVNTSPSAGYIRFYNEFAKRPIMYLNYVYTKAEVKFTNTEKL LTTIHKGLIKALDLGMGQEILVYSPIVSMTKIQKTPLPERKALPIRWITWMSYLEDPRIQFHYDKTLPELQQVPTVTDDIIAKIKHPSEFSMVFYTDGSAIKH PNVNKSHNAGMGIAQVQFKPEFTVINTWSIPLGDHTAQLAEVAAVEFACKKALKIDGPVLIVTDSFYVAESVNKELPYWQSNGFFNNKKKPLKHVSKW KSIADCIQLKPDIIIIHEKGHQPTASTFHTEGNNLADKLATQGSYVVN SFV3L_P27401-Pro 8,114 IPWLMKKPLQLTTLVPLQEYEERLLKQTMLTGSYKEKLQSLFLKYDALWQHWENQVGHRRIKPHHIATGTVNPRPQKQYPINPKAKASIQTVINDLLKQ GVLIQQNSIMNTPVYPVPKPDGKWRMVLDYREVNKTIPLIAAQNQHSAGILSSIFRGKYKTTLDLSNGFWAHSITPESYWLTAFTWLGQQYCWTRLPQ GFLNSPALFTADVVDLLKEVPNVQVYVDDIYISHDDPREHLEQLEKVFSLLLNAGYVVSLKKSEIAQHEVEFLGFNITKEGRGLTETFKQKLLNITPPRDL KQLQSILGLLNFARNFIPNFSELVKPLYNIIATANGKYITWTTDNSQQLQNIISMLNSAENLEERNPEVRLIMKVNTSPSAGYIRFYNEFAKRPIMYLNYVY TKAEVKFTNTEKLLTTIHKGLIKALDLGMGQEILVYSPIVSMTKIQKTPLPERKALPIRWITWMSYLEDPRIQFHYDKTLPELQQVPTVTDDIIAKIKHPSEF SMVFYTDGSAIKHPNVNKSHNAGMGIAQVQFKPEFTVINTWSIPLGDHTAQLAEVAAVEFACKKALKIDGPVLIVTDSFYVAESVNKELPYWQSNGFFN NKKKPLKHVSKWKSIADCIQLKPDIIIIHEKGHQPTASTFHTEGNNLADKLATQGSYVVN SFV3L_P27401-Pro_2mut 8,115 IPWLMKKPLQLTTLVPLQEYEERLLKQTMLTGSYKEKLQSLFLKYDALWQHWENQVGHRRIKPHHIATGTVNPRPQKQYPINPKAKASIQTVINDLLKQ GVLIQQNSIMNTPVYPVPKPDGKWRMVLDYREVNKTIPLIAAQNQHSAGILSSIFRGKYKTTLDLSNGFWAHSITPESYWLTAFTWLGQQYCWTRLPQ GFLNSPALFNADVVDLLKEVPNVQVYVDDIYISHDDPREHLEQLEKVFSLLLNAGYVVSLKKSEIAQHEVEFLGFNITKEGRGLTETFKQKLLNITPPRDL KQLQSILGLLNFARNFIPNFSELVKPLYNIIATAPGKYITWTTDNSQQLQNIISMLNSAENLEERNPEVRLIMKVNTSPSAGYIRFYNEFAKRPIMYLNYVY TKAEVKFTNTEKLLTTIHKGLIKALDLGMGQEILVYSPIVSMTKIQKTPLPERKALPIRWITWMSYLEDPRIQFHYDKTLPELQQVPTVTDDIIAKIKHPSEF SMVFYTDGSAIKHPNVNKSHNAGMGIAQVQFKPEFTVINTWSIPLGDHTAQLAEVAAVEFACKKALKIDGPVLIVTDSFYVAESVNKELPYWQSNGFFN NKKKPLKHVSKWKSIADCIQLKPDIIIIHEKGHQPTASTFHTEGNNLADKLATQGSYVVN SFV3L_P27401-Pro_2mutA 8,116 IPWLMKKPLQLTTLVPLQEYEERLLKQTMLTGSYKEKLQSLFLKYDALWQHWENQVGHRRIKPHHIATGTVNPRPQKQYPINPKAKASIQTVINDLLKQ GVLIQQNSIMNTPVYPVPKPDGKWRMVLDYREVNKTIPLIAAQNQHSAGILSSIFRGKYKTTLDLSNGFWAHSITPESYWLTAFTWLGQQYCWTRLPQ GFLNSPALFNADVVDLLKEVPNVQVYVDDIYISHDDPREHLEQLEKVFSLLLNAGYVVSLKKSEIAQHEVEFLGFNITKEGRGLTETFKQKLLNITPPRDL KQLQSILGKLNFARNFIPNFSELVKPLYNIIATAPGKYITWTTDNSQQLQNIISMLNSAENLEERNPEVRLIMKVNTSPSAGYIRFYNEFAKRPIMYLNYVY TKAEVKFTNTEKLLTTIHKGLIKALDLGMGQEILVYSPIVSMTKIQKTPLPERKALPIRWITWMSYLEDPRIQFHYDKTLPELQQVPTVTDDIIAKIKHPSEF SMVFYTDGSAIKHPNVNKSHNAGMGIAQVQFKPEFTVINTWSIPLGDHTAQLAEVAAVEFACKKALKIDGPVLIVTDSFYVAESVNKELPYWQSNGFFN NKKKPLKHVSKWKSIADCIQLKPDIIIIHEKGHQPTASTFHTEGNNLADKLATQGSYVVN SFVCP_Q87040 8,117 MNPLQLLQPLPAEVKGTKLLAHWNSGATITCIPESFLEDEQPIKQTLIKTIHGEKQQNVYYLTFKVKGRKVEAEVIASPYEYILLSPTDVPWLTQQPLQLTI LVPLQEYQDRILNKTALPEEQKQQLKALFTKYDNLWQHWENQVGHRKIRPHNIATGDYPPRPQKQYPINPKAKPSIQIVIDDLLKQGVLTPQNSTMNTP VYPVPKPDGRWRMVLDYREVNKTIPLTAAQNQHSAGILATIVRQKYKTTLDLANGFWAHPITPDSYWLTAFTWQGKQYCWTRLPQGFLNSPALFTAD AVDLLKEVPNVQVYVDDIYLSHDNPHEHIQQLEKVFQILLQAGYVVSLKKSEIGQRTVEFLGFNITKEGRGLTDTFKTKLLNVTPPKDLKQLQSILGLLNF ARNFIPNFAELVQTLYNLIASSKGKYIEWTEDNTKQLNKVIEALNTASNLEERLPDQRLVIKVNTSPSAGYVRYYNESGKKPIMYLNYVFSKAELKFSMLE KLLTTMHKALIKAMDLAMGQEILVYSPIVSMTKIQKTPLPERKALPIRWITWMTYLEDPRIQFHYDKTLPELKHIPDVYTSSIPPLKHPSQYEGVFCTDGSA IKSPDPTKSNNAGMGIVHAIYNPEYKILNQWSIPLGHHTAQMAEIAAVEFACKKALKVPGPVLVITDSFYVAESANKELPYWKSNGFVNNKKEPLKHISK WKSIAECLSIKPDITIQHEKGHQPINTSIHTEGNALADKLATQGSYVVN SFVCP_Q87040_2mut 8,118 MNPLQLLQPLPAEVKGTKLLAHWNSGATITCIPESFLEDEQPIKQTLIKTIHGEKQQNVYYLTFKVKGRKVEAEVIASPYEYILLSPTDVPWLTQQPLQLTI LVPLQEYQDRILNKTALPEEQKQQLKALFTKYDNLWQHWENQVGHRKIRPHNIATGDYPPRPQKQYPINPKAKPSIQIVIDDLLKQGVLTPQNSTMNTP VYPVPKPDGRWRMVLDYREVNKTIPLTAAQNQHSAGILATIVRQKYKTTLDLANGFWAHPITPDSYWLTAFTWQGKQYCWTRLPQGFLNSPALFNAD AVDLLKEVPNVQVYVDDIYLSHDNPHEHIQQLEKVFQILLQAGYVVSLKKSEIGQRTVEFLGFNITKEGRGLTDTFKTKLLNVTPPKDLKQLQSILGLLNF ARNFIPNFAELVQTLYNLIASSPGKYIEWTEDNTKQLNKVIEALNTASNLEERLPDQRLVIKVNTSPSAGYVRYYNESGKKPIMYLNYVFSKAELKFSMLE KLLTTMHKALIKAMDLAMGQEILVYSPIVSMTKIQKTPLPERKALPIRWITWMTYLEDPRIQFHYDKTLPELKHIPDVYTSSIPPLKHPSQYEGVFCTDGSA IKSPDPTKSNNAGMGIVHAIYNPEYKILNQWSIPLGHHTAQMAEIAAVEFACKKALKVPGPVLVITDSFYVAESANKELPYWKSNGFVNNKKEPLKHISK WKSIAECLSIKPDITIQHEKGHQPINTSIHTEGNALADKLATQGSYVVN SFVCP_Q87040_2mutA 8,119 MNPLQLLQPLPAEVKGTKLLAHWNSGATITCIPESFLEDEQPIKQTLIKTIHGEKQQNVYYLTFKVKGRKVEAEVIASPYEYILLSPTDVPWLTQQPLQLTI LVPLQEYQDRINKTALPEEQKQQLKALFTKYDNLWQHWENQVGHRKIRPHNIATGDYPPRPQKQYPINPKAKPSIQIVIDDLLKQGVLTPQNSTMNTP VYPVPKPDGRWRMVLDYREVNKTIPLTAAQNQHSAGILATIVRQKYKTTLDLANGFWAHPITPDSYWLTAFTWQGKQYCWTRLPQGFLNSPALFNAD AVDLLKEVPNVQVYVDDIYLSHDNPHEHIQQLEKVFQILLQAGYVVSLKKSEIGQRTVEFLGFNITKEGRGLTDTFKTKLLNVTPPKDLKQLQSILGKLNF ARNFIPNFAELVQTLYNLIASSPGKYIEWTEDNTKQLNKVIEALNTASNLEERLPDQRLVIKVNTSPSAGYVRYYNESGKKPIMYLNYVFSKAELKFSMLE KLLTTMHKALIKAMDLAMGQEILVYSPIVSMTKIQKTPLPERKALPIRWITWMTYLEDPRIQFHYDKTLPELKHIPDVYTSSIPPLKHPSQYEGVFCTDGSA IKSPDPTKSNNAGMGIVHAIYNPEYKILNQWSIPLGHHTAQMAEIAAVEFACKKALKVPGPVLVITDSFYVAESANKELPYWKSNGFVNNKKEPLKHISK WKSIAECLSIKPDITIQHEKGHQPINTSIHTEGNALADKLATQGSYVVN SFVCP_Q87040-Pro 8,120 VPWLTQQPLQLTILVPLQEYQDRILNKTALPEEQKQQLKALFTKYDNLWQHWENQVGHRKIRPHNIATGDYPPRPQKQYPINPKAKPSIQIVIDDLLKQG VLTPQNSTMNTPVYPVPKPDGRWRMVLDYREVNKTIPLTAAQNQHSAGILATIVRQKYKTTLDLANGFWAHPITPDSYWLTAFTWQGKQYCWTRLPQ GFLNSPALFTADAVDLLKEVPNVQVYVDDIYLSHDNPHEHIQQLEKVFQILLQAGYVVSLKKSEIGQRTVEFLGFNITKEGRGLTDTFKTKLLNVTPPKDL KQLQSILGLLNFARNFIPNFAELVQTLYNLIASSKGKYIEWTEDNTKQLNKVIEALNTASNLEERLPDQRLVIKVNTSPSAGYVRYYNESGKKPIMYLNYV FSKAELKFSMLEKLLTTMHKALIKAMDLAMGQEILVYSPIVSMTKIQKTPLPERKALPIRWITWMTYLEDPRIQFHYDKTLPELKHIPDVYTSSIPPLKHPS QYEGVFCTDGSAIKSPDPTKSNNAGMGIVHAIYNPEYKILNQWSIPLGHHTAQMAEIAAVEFACKKALKVPGPVLVITDSFYVAESANKELPYWKSNGF VNNKKEPLKHISKWKSIAECLSIKPDITIQHEKGHQPINTSIHTEGNALADKLATQGSYVVN SFVCP_Q87040-Pro_2mut 8,121 VPWLTQQPLQLTILVPLQEYQDRILNKTALPEEQKQQLKALFTKYDNLWQHWENQVGHRKIRPHNIATGDYPPRPQKQYPINPKAKPSIQIVIDDLLKQG VLTPQNSTMNTPVYPVPKPDGRWRMVLDYREVNKTIPLTAAQNQHSAGILATIVRQKYKTTLDLANGFWAHPITPDSYWLTAFTWQGKQYCWTRLPQ GFLNSPALFNADAVDLLKEVPNVQVYVDDIYLSHDNPHEHIQQLEKVFQILLQAGYVVSLKKSEIGQRTVEFLGFNITKEGRGLTDTFKTKLLNVTPPKDL KQLQSILGLLNFARNFIPNFAELVQTLYNLIASSPGKYIEWTEDNTKQLNKVIEALNTASNLEERLPDQRLVIKVNTSPSAGYVRYYNESGKKPIMYLNYV FSKAELKFSMLEKLLTTMHKALIKAMDLAMGQEILVYSPIVSMTKIQKTPLPERKALPIRWITWMTYLEDPRIQFHYDKTLPELKHIPDVYTSSIPPLKHPS QYEGVFCTDGSAIKSPDPTKSNNAGMGIVHAIYNPEYKILNQWSIPLGHHTAQMAEIAAVEFACKKALKVPGPVLVITDSFYVAESANKELPYWKSNGF VNNKKEPLKHISKWKSIAECLSIKPDITIQHEKGHQPINTSIHTEGNALADKLATQGSYVVN SFVCP_Q87040-Pro_2mutA 8,122 VPWLTQQPLQLTILVPLQEYQDRILNKTALPEEQKQQLKALFTKYDNLWQHWENQVGHRKIRPHNIATGDYPPRPQKQYPINPKAKPSIQIVIDDLLKQG VLTPQNSTMNTPVYPVPKPDGRWRMVLDYREVNKTIPLTAAQNQHSAGILATIVRQKYKTTLDLANGFWAHPITPDSYWLTAFTWQGKQYCWTRLPQ GFLNSPALFNADAVDLLKEVPNVQVYVDDIYLSHDNPHEHIQQLEKVFQILLQAGYVVSLKKSEIGQRTVEFLGFNITKEGRGLTDTFKTKLLNVTPPKDL KQLQSILGKLNFARNFIPNFAELVQTLYNLIASSPGKYIEWTEDNTKQLNKVIEALNTASNLEERLPDQRLVIKVNTSPSAGYVRYYNESGKKPIMYLNYV FSKAELKFSMLEKLLTTMHKALIKAMDLAMGQEILVYSPIVSMTKIQKTPLPERKALPIRWITWMTYLEDPRIQFHYDKTLPELKHIPDVYTSSIPPLKHPS QYEGVFCTDGSAIKSPDPTKSNNAGMGIVHAIYNPEYKILNQWSIPLGHHTAQMAEIAAVEFACKKALKVPGPVLVITDSFYVAESANKELPYWKSNGF VNNKKEPLKHISKWKSIAECLSIKPDITIQHEKGHQPINTSIHTEGNALADKLATQGSYVVN SMRVH_P03364 8,123 PRSRAIDIPVPHADKISWKITDPVWVDQWPLTYEKTLAAIALVQEQLAAGHIEPTNSPWNTPIFIIKKKSGSWRLLQDLRAVNKVMVPMGALQPGLPSPV AIPLNYHKIVIDLKDCFFTIPLHPEDRPYFAFSVPQINFQSPMPRYQWKVLPQGMANSPTLCQKFVAAAIAPVRSQWPEAYILHYMDDILLACDSAEAAK ACYAHIISCLTSYGLKIAPDKVQVSEPFSYLGFELHHQQVFTPRVCLKTDHLKTLNDFQKLLGDIQWLRPYLKLPTSALVPLNNILKGDPNPLSVRALTPE AKQSLALINKAIQNQSVQQISYNLPLVLLLLPTPHTPTAVFWQPNGTDPTKNGSPLLWLHLPASPSKVLLTYPSLLAMLIIKGRYTGRQLFGRDPHSIIIPY TQDQLTWLLQTSDEWAIALSSFTGDIDNHYPSDPVIQFAKLHQFIFPKITKCAPIPQATLVFTDGSSNGIAAYVIDNQPISIKSPYLSAQLVELYAILQVFTV LAHQPFNLYTDSAYIAQSVPLLETVPFIKSSTNATPLFSKLQQLILNRQHPFFIGHLRAHLNLPGPLAEGNALADAATQIFPIISD SMRVH_P03364_2mut 8,124 PRSRAIDIPVPHADKISWKITDPVWVDQWPLTYEKTLAAIALVQEQLAAGHIEPTNSPWNTPIFIIKKKSGSWRLLQDLRAVNKVMVPMGALQPGLPSPV AIPLNYHKIVIDLKDCFFTIPLHPEDRPYFAFSVPQINFQSPMPRYQWKVLPQGMANSPTLCQKFVAAAIAPVRSQWPEAYILHYMDDILLACDSAEAAK ACYAHIISCLTSYGLKIAPDKVQVSEPFSYLGFELHHQQVFTPRVCLKTDHLKTLNDFQKLLGDIQWLRPYLKLPTSALVPLNNILKPDPNPLSVRALTPE AKQSLALINKAIQNQSVQQISYNLPLVLLLLPTPHTPTAVFWQPNGTDPTKNGSPLLWLHLPASPSKVLLTYPSLLAMLIIKGRYTGRQLFGRDPHSIIIPY TQDQLTWLLQTSDEWAIALSSFTGDIDNHYPSDPVIQFAKLHQFIFPKITKCAPIPQATLVFTDGSSNGIAAYVIDNQPISIKSPYLSAQLVELYAILQVFTV LAHQPFNLYTDSAYIAQSVPLLETVPFIKSSTNATPLFSKLQQLILNRQHPFFIGHLRAHLNLPGPLAEGNALADAATQIFPIISD SMRVH_P03364_2mutB 8,125 PRSRAIDIPVPHADKISWKITDPVWVDQWPLTYEKTLAAIALVQEQLAAGHIEPTNSPWNTPIFIIKKKSGSWRLLQDLRAVNKVMVPMGALQPGLPSPV APPLNYHKIVIDLKDCFFTIPLHPEDRPYFAFSVPQINFQSPMPRYQWKVLPQGMANSPTLCQKFVAAAIAPVRSQWPEAYILHYMDDILLACDSAEAAK ACYAHIISCLTSYGLKIAPDKVQVSEPFSYLGFELHHQQVFTPRVCLKTDHLKTLNDFQKLLGDIQWLRPYLKLPTSALVPLNNILKPDPNPLSVRALTPE AKQSLALINKAIQNQSVQQISYNLPLVLLLLPTPHTPTAVFWQPNGTDPTKNGSPLLWLHLPASPSKVLLTYPSLLAMLIIKGRYTGRQLFGRDPHSIIIPY TQDQLTWLLQTSDEWAIALSSFTGDIDNHYPSDPVIQFAKLHQFIFPKITKCAPIPQATLVFTDGSSNGIAAYVIDNQPISIKSPYLSAQLVELYAILQVFTV LAHQPFNLYTDSAYIAQSVPLLETVPFIKSSTNATPLFSKLQQLILNRQHPFFIGHLRAHLNLPGPLAEGNALADAATQIFPIISD SRV2_P51517 8,126 LATAVDILAPQRYADPITWKSDEPVWVDQWPLTQEKLAAAQQLVQEQLQAGHIIESNSPWNTPIFVIKKKSGKWRLLQDLRAVNATMVLMGALQPGLP SPVAIPQGYFKIVIDLKDCFFTIPLQPVDQKRFAFSLPSTNFKQPMKRYQWKVLPQGMANSPTLCQKYVAAAIEPVRKSWAQMYIIHYMDDILIAGKLGE QVLQCFAQLKQALTTTGLQIAPEKVQLQDPYTYLGFQINGPKITNQKAVIRRDKLQTLNDFQKLLGDINWLRPYLHLTTGDLKPLFDILKGDSNPNSPRS LSEAALASLQKVETAIAEQFVTQIDYTQPLTFLIFNTTLTPTGLFWQNNPVMWVHLPASPKKVLLPYYDAIADLIILGRDNSKKYFGLEPSTIIQPYSKSQIH WLMQNTETWPIACASYAGNIDNHYPPNKLIQFCKLHAVVFPRIISKTPLDNALLVFTDGSSTGIAAYTFEKTTVRFKTSHTSAQLVELQALIAVLSAFPHR ALNVYTDSAYLAHSIPLLETVSHIKHISDTAKFFLQCQQLIYNRSIPFYLGHIRAHSGLPGPLSQGNHITDLATKVVATTLTT SRV2_P51517_2mutB 8,127 LATAVDILAPQRYADPITWKSDEPVWVDQWPLTQEKLAAAQQLVQEQLQAGHIIESNSPWNTPIFVIKKKSGKWRLLQDLRAVNATMVLMGALQPGLP SPVAPPQGYFKIVIDLKDCFFTIPLQPVDQKRFAFSLPSTNFKQPMKRYQWKVLPQGMANSPTLCQKYVAAAIEPVRKSWAQMYIIHYMDDILIAGKLGE QVLQCFAQLKQALTTTGLQIAPEKVQLQDPYTYLGFQINGPKITNQKAVIRRDKLQTLNDFQKLLGDINWLRPYLHLTTGDLKPLFDILKGDSNPNSPRS LSEAALASLQKVETAIAEQFVTQIDYTQPLTFLIFNTTLTPTGLFWQNNPVMWVHLPASPKKVLLPYYDAIADLIILGRDNSKKYFGLEPSTIIQPYSKSQIH WLMQNTETWPIACASYAGNIDNHYPPNKLIQFCKLHAVVFPRIISKTPLDNALLVFTDGSSTGIAAYTFEKTTVRFKTSHTSAQLVELQALIAVLSAFPHR ALNVYTDSAYLAHSIPLLETVSHIKHISDTAKFFLQCQQLIYNRSIPFYLGHIRAHSGLPGPLSQGNHITDLATKVVATTLTT WDSV_O92815 8,128 SCQTKNTLNIDEYLLQFPDQLWASLPTDIGRMLVPPITIKIKDNASLPSIRQYPLPKDKTEGLRPLISSLENQGILIKCHSPCNTPIFPIKKAGRDEYRMIHD LRAINNIVAPLTAVVASPTTVLSNLAPSLHWFTVIDLSNAFFSVPIHKDSQYLFAFTFEGHQYTWTVLPQGFIHSPTLFSQALYQSLHKIKFKISSEICIYMD DVLIASKDRDTNLKDTAVMLQHLASEGHKVSKKKLQLCQQEVVYLGQLLTPEGRKILPDRKVTVSQFQQPTTIRQIRAFLGLVGYCRHWIPEFSIHSKFL EKQLKKDTAEPFQLDDQQVEAFNKLKHAITTAPVLVVPDPAKPFQLYTSHSEHASIAVLTQKHAGRTRPIAFLSSKFDAIESGLPPCLKACASIHRSLTQA DSFILGAPLIIYTTHAICTLLQRDRSQLVTASRFSKWEADLLRPELTFVACSAVSPAHLYMQSCENNIPPHDCVLLTHTISRPRPDLSDLPIPDPDMTLFSD GSYTTGRGGAAVVMHRPVTDDFIIIHQQPGGASAQTAELLALAAACHLATDKTVNIYTDSRYAYGVVHDFGHLWMHRGFVTSAGTPIKNHKEIEYLLKQ IMKPKQVSVIKIEAHTKGVSMEVRGNAAADEAAKNAVFLVQR WDSV_O92815_2mut 8,129 SCQTKNTLNIDEYLLQFPDQLWASLPTDIGRMLVPPITIKIKDNASLPSIRQYPLPKDKTEGLRPLISSLENQGILIKCHSPCNTPIFPIKKAGRDEYRMIHD LRAINNIVAPLTAWASPTTVLSNLAPSLHWFTVIDLSNAFFSVPIHKDSQYLFAFTFEGHQYTWTVLPQGFIHSPTLFNQALYQSLHKIKFKISSEICIYMD DVLIASKDRDTNLKDTAVMLQHLASEGHKVSKKKLQLCQQEVVYLGQLLTPEGRKILPDRKVTVSQFQQPTTIRQIRAFLGLVGYCRHWIPEFSIHSKFL EKQLKPDTAEPFQLDDQQVEAFNKLKHAITTAPVLVVPDPAKPFQLYTSHSEHASIAVLTQKHAGRTRPIAFLSSKFDAIESGLPPCLKACASIHRSLTQA DSFILGAPLIIYTTHAICTLLQRDRSQLVTASRFSKWEADLLRPELTFVACSAVSPAHLYMQSCENNIPPHDCVLLTHTISRPRPDLSDLPIPDPDMTLFSD GSYTTGRGGAAVVMHRPVTDDFIIIHQQPGGASAQTAELLALAAACHLATDKTVNIYTDSRYAYGWHDFGHLWMHRGFVTSAGTPIKNHKEIEYLLKQ IMKPKQVSVIKIEAHTKGVSMEVRGNAAADEAAKNAVFLVQR WDSV_O92815_2mutA 8,130 SCQTKNTLNIDEYLLQFPDQLWASLPTDIGRMLVPPITIKIKDNASLPSIRQYPLPKDKTEGLRPLISSLENQGILIKCHSPCNTPIFPIKKAGRDEYRMIHD LRAINNIVAPLTAVVASPTTVLSNLAPSLHWFTVIDLSNAFFSVPIHKDSQYLFAFTFEGHQYTWTVLPQGFIHSPTLFNQALYQSLHKIKFKISSEICIYMD DVLIASKDRDTNLKDTAVMLQHLASEGHKVSKKKLQLCQQEVVYLGQLLTPEGRKILPDRKVTVSQFQQPTTIRQIRAFLGKVGYCRHFIPEFSIHSKFL EKQLKPDTAEPFQLDDQQVEAFNKLKHAITTAPVLVVPDPAKPFQLYTSHSEHASIAVLTQKHAGRTRPIAFLSSKFDAIESGLPPCLKACASIHRSLTQA DSFILGAPLIIYTTHAICTLLQRDRSQLVTASRFSKWEADLLRPELTFVACSAVSPAHLYMQSCENNIPPHDCVLLTHTISRPRPDLSDLPIPDPDMTLFSD GSYTTGRGGAAVVMHRPVTDDFIIIHQQPGGASAQTAELLALAAACHLATDKTVNIYTDSRYAYGWHDFGHLWMHRGFVTSAGTPIKNHKEIEYLLKQ IMKPKQVSVIKIEAHTKGVSMEVRGNAAADEAAKNAVFLVQR WMSV_P03359 8,131 VLNLEEEYRLHEKPVPSSIDPSWLQLFPTVWAERAGMGLANQVPPVVVELRSGASPVAVRQYPMSKEAREGIRPHIQRFLDLGVLVPCQSPWNTPLL PVKKPGTNDYRPVQDLREINKRVQDIHPTVPNPYNLLSSLPPSHTWYSVLDLKDAFFCLKLHPNSQPLFAFEWRDPEKGNTGQLTWTRLPQGFKNSP TLFDEALHRDLAPFRALNPQVVLLQYVDDLLVAAPTYRDCKEGTQKLLQELSKLGYRVSAKKAQLCQKEVTYLGYLLKEGKRWLTPARKATVMKIPPP TTPRQVREFLGTAGFCRLWIPGFASLAAPLYPLTKESIPFIWTEEHQKAFDRIKEALLSAPALALPDLTKPFTLYVDERAGVARGVLTQTLGPWRRPVAY LSKKLDPVASGWPTCLKAVAAVALLLKDADKLTLGQNVTVIASHSLESIVRQPPDRWMTNARMTHYQSLLLNERVSFAPPAVLNPATLLPVESEATPVH RCSEILAEETGTRRDLKDQPLPGVPAWYTDGSSFIAEGKRRAGAAIVDGKRTVWASSLPEGTSAQKAELVALTQALRLAEGKDINIYTDSRYAFATAHI HGAIYKQRGLLTSAGKDIKNKEEILALLEAIHLPKRVAIIHCPGHQKGNDPVATGNRRADEAAKQAALSTRVLAETTKP WMSV_P03359_3mut 8,132 VLNLEEEYRLHEKPVPSSIDPSWLQLFPTVWAERAGMGLANQVPPVVVELRSGASPVAVRQYPMSKEAREGIRPHIQRFLDLGVLVPCQSPWNTPLL PVKKPGTNDYRPVQDLREINKRVQDIHPTVPNPYNLLSSLPPSHTWYSVLDLKDAFFCLKLHPNSQPLFAFEWRDPEKGNTGQLTWTRLPQGFKNSP TLFNEALHRDLAPFRALNPQVVLLQYVDDLLVAAPTYRDCKEGTQKLLQELSKLGYRVSAKKAQLCQKEVTYLGYLLKEGKRWLTPARKATVMKIPPP TTPRQVREFLGTAGFCRLWIPGFASLAAPLYPLTKPSIPFIWTEEHQKAFDRIKEALLSAPALALPDLTKPFTLYVDERAGVARGVLTQTLGPWRRPVAY LSKKLDPVASGWPTCLKAVAAVALLLKDADKLTLGQNVTVIASHSLESIVRQPPDRWMTNARMTHYQSLLLNERVSFAPPAVLNPATLLPVESEATPVH RCSEILAEETGTRRDLKDQPLPGVPAWYTDGSSFIAEGKRRAGAAIVDGKRTVWASSLPEGTSAQKAELVALTQALRLAEGKDINIYTDSRYAFATAHI HGAIYKQRGWLTSAGKDIKNKEEILALLEAIHLPKRVAIIHCPGHQKGNDPVATGNRRADEAAKQAALSTRVLAETTKP WMSV_P03359_3mutA 8,133 VLNLEEEYRLHEKPVPSSIDPSWLQLFPTVWAERAGMGLANQVPPVVVELRSGASPVAVRQYPMSKEAREGIRPHIQRFLDLGVLVPCQSPWNTPLL PVKKPGTNDYRPVQDLREINKRVQDIHPTVPNPYNLLSSLPPSHTWYSVLDLKDAFFCLKLHPNSQPLFAFEWRDPEKGNTGQLTWTRLPQGFKNSP TLFNEALHRDLAPFRALNPQVVLLQYVDDLLVAAPTYRDCKEGTQKLLQELSKLGYRVSAKKAQLCQKEVTYLGYLLKEGKRWLTPARKATVMKIPPP TTPRQVREFLGKAGFCRLFIPGFASLAAPLYPLTKPSIPFIWTEEHQKAFDRIKEALLSAPALALPDLTKPFTLYVDERAGVARGVLTQTLGPWRRPVAY LSKKLDPVASGWPTCLKAVAAVALLLKDADKLTLGQNVTVIASHSLESIVRQPPDRWMTNARMTHYQSLLLNERVSFAPPAVLNPATLLPVESEATPVH RCSEILAEETGTRRDLKDQPLPGVPAWYTDGSSFIAEGKRRAGAAIVDGKRTVWASSLPEGTSAQKAELVALTQALRLAEGKDINIYTDSRYAFATAHI HGAIYKQRGWLTSAGKDIKNKEEILALLEAIHLPKRVAIIHCPGHQKGNDPVATGNRRADEAAKQAALSTRVLAETTKP XMRV6_A1Z651 8,134 TLNIEDEYRLHETSKEPDVPLGSTWLSDFPQAWAETGGMGLAVRQAPLIIPLKATSTPVSIKQYPMSQEARLGIKPHIQRLLDQGILVPCQSPWNTPLLP VKKPGTNDYRPVQDLREVNKRVEDIHPTVPNPYNLLSGLPPSHQWYTVLDLKDAFFCLRLHPTSQPLFAFEWRDPEMGISGQLTWTRLPQGFKNSPT LFDEALHRDLADFRIQHPDLILLQYVDDLLLAATSEQDCQRGTRALLQTLGNLGYRASAKKAQICQKQVKYLGYLLKEGQRWLTEARKETVMGQPTPK TPRQLREFLGTAGFCRLWIPGFAEMAAPLYPLTKTGTLFNWGPDQQKAYQEIKQALLTAPALGLPDLTKPFELFVDEKQGYAKGVLTQKLGPWRRPVA YLSKKLDPVAAGWPPCLRMVAAIAVLTKDAGKLTMGQPLVILAPHAVEALVKQPPDRWLSNARMTHYQAMLLDTDRVQFGPVVALNPATLLPLPEKEA PHDCLEILAETHGTRPDLTDQPIPDADYTWYTDGSSFLQEGQRRAGAAVTTETEVIWARALPAGTSAQRAELIALTQALKMAEGKKLNVYTDSRYAFAT AHVHGEIYRRRGLLTSEGREIKNKNEILALLKALFLPKRLSIIHCPGHQKGNSAEARGNRMADQAAREAAMKAVLETSTLL XMRV6_A1Z651_3mut 8,135 TLNIEDEYRLHETSKEPDVPLGSTWLSDFPQAWAETGGMGLAVRQAPLIIPLKATSTPVSIKQYPMSQEARLGIKPHIQRLLDQGILVPCQSPWNTPLLP VKKPGTNDYRPVQDLREVNKRVEDIHPTVPNPYNLLSGLPPSHQWYTVLDLKDAFFCLRLHPTSQPLFAFEWRDPEMGISGQLTWTRLPQGFKNSPT LFNEALHRDLADFRIQHPDLILLQYVDDLLLAATSEQDCQRGTRALLQTLGNLGYRASAKKAQICQKQVKYLGYLLKEGQRWLTEARKETVMGQPTPK TPRQLREFLGTAGFCRLWIPGFAEMAAPLYPLTKPGTLFNWGPDQQKAYQEIKQALLTAPALGLPDLTKPFELFVDEKQGYAKGVLTQKLGPWRRPV AYLSKKLDPVAAGWPPCLRMVAAIAVLTKDAGKLTMGQPLVILAPHAVEALVKQPPDRWLSNARMTHYQAMLLDTDRVQFGPWVALNPATLLPLPEKE APHDCLEILAETHGTRPDLTDQPIPDADYTWYTDGSSFLQEGQRRAGAAVTTETEVIWARALPAGTSAQRAELIALTQALKMAEGKKLNVYTDSRYAF ATAHVHGEIYRRRGWLTSEGREIKNKNEILALLKALFLPKRLSIIHCPGHQKGNSAEARGNRMADQAAREAAMKAVLETSTLL XMRV6_A1Z651_3mutA 8,136 TLNIEDEYRLHETSKEPDVPLGSTWLSDFPQAWAETGGMGLAVRQAPLIIPLKATSTPVSIKQYPMSQEARLGIKPHIQRLLDQGILVPCQSPWNTPLLP VKKPGTNDYRPVQDLREVNKRVEDIHPTVPNPYNLLSGLPPSHQWYTVLDLKDAFFCLRLHPTSQPLFAFEWRDPEMGISGQLTWTRLPQGFKNSPT LFNEALHRDLADFRIQHPDLILLQYVDDLLLAATSEQDCQRGTRALLQTLGNLGYRASAKKAQICQKQVKYLGYLLKEGQRWLTEARKETVMGQPTPK TPRQLREFLGKAGFCRLFIPGFAEMAAPLYPLTKPGTLFNWGPDQQKAYQEIKQALLTAPALGLPDLTKPFELFVDEKQGYAKGVLTQKLGPWRRPVA YLSKKLDPVAAGWPPCLRMVAAIAVLTKDAGKLTMGQPLVILAPHAVEALVKQPPDRWLSNARMTHYQAMLLDTDRVQFGPWVALNPATLLPLPEKEA PHDCLEILAETHGTRPDLTDQPIPDADYTWYTDGSSFLQEGQRRAGAAVTTETEVIWARALPAGTSAQRAELIALTQALKMAEGKKLNVYTDSRYAFAT AHVHGEIYRRRGWLTSEGREIKNKNEILALLKALFLPKRLSIIHCPGHQKGNSAEARGNRMADQAAREAAMKAVLETSTLL

In some embodiments, reverse transcriptase domains are modified, for example by site-specific mutation. In some embodiments, reverse transcriptase domains are engineered to have improved properties, e.g. SuperScript IV (SSIV) reverse transcriptase derived from the MMLV RT. In some embodiments, the reverse transcriptase domain may be engineered to have lower error rates, e.g., as described in WO2001068895, incorporated herein by reference. In some embodiments, the reverse transcriptase domain may be engineered to be more thermostable. In some embodiments, the reverse transcriptase domain may be engineered to be more processive. In some embodiments, the reverse transcriptase domain may be engineered to have tolerance to inhibitors. In some embodiments, the reverse transcriptase domain may be engineered to be faster. In some embodiments, the reverse transcriptase domain may be engineered to better tolerate modified nucleotides in the RNA template. In some embodiments, the reverse transcriptase domain may be engineered to insert modified DNA nucleotides. In some embodiments, the reverse transcriptase domain is engineered to bind a template RNA. In some embodiments, one or more mutations are chosen from D200N, L603W, T330P, D524G, E562Q, D583N, P53L, S67R, E67K, T197A, H204R, E302K, F309N, W313F, L435G, N454K, H594Q, L671P, E69K, H8Y, T306K, or D653N in the RT domain of murine leukemia virus reverse transcriptase or a corresponding mutation at a corresponding position of another RT domain.

In some embodiments, an RT domain (e.g., as listed in Table 6) comprises one or more mutations as listed in Table 2 below. In some embodiment, an RT domain as listed in Table 6 comprises one, two, three, four, five, or six of the mutations listed in the corresponding row of Table 2 below.

TABLE 2 Exemplary RT domain mutations (relative to corresponding wild- type sequences as listed in the corresponding row of Table 6) RT Domain Name Mutation(s) AVIRE_P03360 AVIRE_P03360_3mut D200N G330P L605W AVIRE_P03360_3mutA D200N G330P L605W T306K W313F BAEVM_P10272 BAEVM_P10272_3mut D198N E328P L602W BAEVM_P10272_3mutA D198N E328P L602W T304K W311F BLVAU_P25059 BLVAU_P25059_2mut E159Q G286P BLVJ_P03361 BLVJ_P03361_2mut E159Q L524W BLVJ_P03361_2mutB E159Q L524W I97P FFV_O93209 D21N FFV_O93209_2mut D21N T293N T419P FFV_O93209_2mutA D21N T293N T419P L393K FFV_O93209-Pro FFV_O93209-Pro_2mut T207N T333P FFV_O93209-Pro_2mutA T207N T333P L307K FLV_P10273 FLV_P10273_3mut D199N L602W FLV_P10273_3mutA D199N L602W T305K W312F FOAMV_P14350 D24N FOAMV_P14350_2mut D24N T296N S420P FOAMV_P14350_2mutA D24N T296N S420P L396K FOAMV_P14350-Pro FOAMV_P14350-Pro_2mut T207N S331P FOAMV_P14350-Pro_2mutA T207N S331P L307K GALV_P21414 GALV_P21414_3mut D198N E328P L600W GALV_P21414_3mutA D198N E328P L600W T304K W311F HTL1A_P03362 HTL1A_P03362_2mut E152Q R279P HTL1A_P03362_2mutB E152Q R279P L90P HTL1C_P14078 HTL1C_P14078_2mut E152Q R279P HTL1L_P0C211 HTL1L_P0C211_2mut E149Q L527W HTL1L_P0C211_2mutB E149Q L527W L87P HTL32_Q0R5R2 HTL32_Q0R5R2_2mut E149Q L526W HTL32_Q0R5R2_2mutB E149Q L526W L87P HTL3P_Q4U0X6 HTL3P_Q4U0X6_2mut E149Q L526W HTL3P_Q4U0X6_2mutB E149Q L526W L87P HTLV2_P03363_2mut E147Q G274P JSRV_P31623 JSRV_P31623_2mutB A100P KORV_Q9TTC1 D32N KORV_Q9TTC1_3mut D32N D322N E452P L724W KORV_Q9TTC1_3mutA D32N D322N E452P L724W T428K W435F KORV_Q9TTC1-Pro KORV_Q9TTC1-Pro_3mut D231N E361P L633W KORV_Q9TTC1-Pro_3mutA D231N E361P L633W T337K W344F MLVAV_P03356 MLVAV_P03356_3mut D200N T330P L603W MLVAV_P03356_3mutA D200N T330P L603W T306K W313F MLVBM_Q7SVK7 MLVBM_Q7SVK7 MLVBM_Q7SVK7_3mut D200N T330P L603W MLVBM_Q7SVK7_3mut D200N T330P L603W MLVBM_Q7SVK7_3mutA_WS D199N T329P L602W T305K W312F MLVBM_Q7SVK7_3mutA_WS D199N T329P L602W T305K W312F MLVCB_P08361 MLVCB_P08361_3mut D200N T330P L603W MLVCB_P08361_3mutA D200N T330P L603W T306K W313F MLVF5_P26810 MLVF5_P26810_3mut D200N T330P L603W MLVF5_P26810_3mutA D200N T330P L603W T306K W313F MLVFF_P26809_3mut D200N T330P L603W MLVFF_P26809_3mutA D200N T330P L603W T306K W313F MLVMS_P03355 MLVMS_P03355 MLVMS_P03355_3mut D200N T330P L603W MLVMS_P03355_3mut D200N T330P L603W MLVMS_P03355_3mutA_WS D200N T330P L603W T306K W313F MLVMS_P03355_3mutA_WS D200N T330P L603W T306K W313F MLVMS_P03355_PLV919 D200N T330P L603W T306K W313F H8Y MLVMS_P03355_PLV919 D200N T330P L603W T306K W313F H8Y MLVRD_P11227 MLVRD_P11227_3mut D200N T330P L603W MMTVB_P03365 D26N MMTVB_P03365 D26N MMTVB_P03365_2mut D26N G401P MMTVB_P03365_2mut_WS G400P MMTVB_P03365_2mut_WS G400P MMTVB_P03365_2mutB D26N G401P V215P MMTVB_P03365_2mutB D26N G401P V215P MMTVB_P03365_2mutB_WS G400P V212P MMTVB_P03365_2mutB_WS G400P V212P MMTVB_P03365_WS MMTVB_P03365_WS MMTVB_P03365-Pro MMTVB_P03365-Pro MMTVB_P03365-Pro_2mut G309P MMTVB_P03365-Pro_2mut G309P MMTVB_P03365-Pro_2mutB G309P V123P MMTVB_P03365-Pro_2mutB G309P V123P MPMV_P07572 MPMV_P07572_2mutB G289P I103P PERV_Q4VFZ2 PERV_Q4VFZ2 PERV_Q4VFZ2_3mut D199N E329P L602W PERV_Q4VFZ2_3mut D199N E329P L602W PERV_Q4VFZ2_3mutA_WS D196N E326P L599W T302K W309F PERV_Q4VFZ2_3mutA_WS D196N E326P L599W T302K W309F SFV1_P23074 D24N SFV1_P23074_2mut D24N T296N N420P SFV1_P23074_2mutA D24N T296N N420P L396K SFV1_P23074-Pro SFV1_P23074-Pro_2mut T207N N331P SFV1_P23074-Pro_2mutA T207N N331P L307K SFV3L_P27401 D24N SFV3L_P27401_2mut D24N T296N N422P SFV3L_P27401_2mutA D24N T296N N422P L396K SFV3L_P27401-Pro SFV3L_P27401-Pro_2mut T307N N333P SFV3L_P27401-Pro_2mutA T307N N333P L307K SFVCP_Q87040 D24N SFVCP_Q87040_2mut D24N T296N K422P SFVCP_Q87040_2mutA D24N T296N K422P L396K SFVCP_Q87040-Pro SFVCP_Q87040-Pro_2mut T207N K333P SFVCP_Q87040-Pro_2mutA T207N K333P L307K SMRVH_P03364 SMRVH_P03364_2mut G288P SMRVH_P03364_2mutB G288P I102P SRV2_P51517 SRV2_P51517_2mutB I103P WDSV_O92815 WDSV_O92815_2mut S183N K312P WDSV_O92815_2mutA S183N K312P L288K W295F WMSV_P03359 WMSV_P03359_3mut D198N E328P L600W WMSV_P03359_3mutA D198N E328P L600W T304K W311F XMRV6_A1Z651 XMRV6_A1Z651_3mut D200N T330P L603W XMRV6_A1Z651_3mutA D200N T330P L603W T306K W313F

In some embodiments, a gene modifying polypeptide comprises the RT domain from a retroviral reverse transcriptase, e.g., a wild-type M-MLV RT, e.g., comprising the following sequence:

M-MLV (WT): (SEQ ID NO: 5002) TLNIEDEYRLHETSKEPDVSLGSTWLSDFPQAWAETGGMGLAVRQAPLI IPLKATSTPVSIKQYPMSQEARLGIKPHIQRLLDQGILVPCQSPWNTPL LPVKKPGTNDYRPVQDLREVNKRVEDIHPTVPNPYNLLSGLPPSHQWYT VLDLKDAFFCLRLHPTSQPLFAFEWRDPEMGISGQLTWTRLPQGFKNSP TLFDEALHRDLADFRIQHPDLILLQYVDDLLLAATSELDCQQGTRALLQ TLGNLGYRASAKKAQICQKQVKYLGYLLKEGQRWLTEARKETVMGQPTP KTPRQLREFLGTAGFCRLWIPGFAEMAAPLYPLTKTGTLFNWGPDQQKA YQEIKQALLTAPALGLPDLTKPFELFVDEKQGYAKGVLTQKLGPWRRPV AYLSKKLDPVAAGWPPCLRMVAAIAVLTKDAGKLTMGQPLVILAPHAVE ALVKQPPDRWLSNARMTHYQALLLDTDRVQFGPVVALNPATLLPLPEEG LQHNCLDILAEAHGTRPDLTDQPLPDADHTWYTDGSSLLQEGQRKAGAA VTTETEVIWAKALPAGTSAQRAELIALTQALKMAEGKKLNVYTDSRYAF ATAHIHGEIYRRRGLLTSEGKEIKNKDEILALLKALFLPKRLSIIHCPG HQKGHSAEARGNRMADQAARKAAITETPDTSTLLI

In some embodiments, a gene modifying polypeptide comprises the RT domain from a retroviral reverse transcriptase, e.g., an M-MLV RT, e.g., comprising the following sequence:

(SEQ ID NO: 5003) TLNIEDEHRLHETSKEPDVSLGSTWLSDFPQAWAETGGMGLAVRQAPLI IPLKATSTPVSIKQYPMSQEARLGIKPHIQRLLDQGILVPCQSPWNTPL LPVKKPGTNDYRPVQDLREVNKRVEDIHPTVPNPYNLLSGLPPSHQWYT VLDLKDAFFCLRLHPTSQPLFAFEWRDPEMGISGQLTWTRLPQGFKNSP TLFDEALHRDLADFRIQHPDLILLQYVDDLLLAATSELDCQQGTRALLQ TLGNLGYRASAKKAQICQKQVKYLGYLLKEGQRWLTEARKETVMGQPTP KTPRQLREFLGTAGFCRLWIPGFAEMAAPLYPLTKTGTLFNWGPDQQKA YQEIKQALLTAPALGLPDLTKPFELFVDEKQGYAKGVLTQKLGPWRRPV AYLSKKLDPVAAGWPPCLRMVAAIAVLTKDAGKLTMGQPLVILAPHAVE ALVKQPPDRWLSNARMTHYQALLLDTDRVQFGPVVALNPATLLPLPEEG LQHNCLDILAEAHGTRPDLTDQPLPDADHTWYTDGSSLLQEGQRKAGAA VTTETEVIWAKALPAGTSAQRAELIALTQALKMAEGKKLNVYTDSRYAF ATAHIHGEIYRRRGLLTSEGKEIKNKDEILALLKALFLPKRLSIIHCPG HQKGHSAEARGNRMADQAARKAAITETPDTSTLL

In some embodiments, a gene modifying polypeptide comprises the RT domain from a retroviral reverse transcriptase comprising the sequence of amino acids 659-1329 of NP_057933. In embodiments, the gene modifying polypeptide further comprises one additional amino acid at the N-terminus of the sequence of amino acids 659-1329 of NP_057933, e.g., as shown below:

(SEQ ID NO: 5004) TLNIEDEHRLHETSKEPDVSLGSTWLSDFPQAWAETGGMGLAVRQAPLI IPLKATSTPVSIKQYPMSQEARLGIKPHIQRLLDQGILVPCQSPWNTPL LPVKKPGTNDYRPVQDLREVNKRVEDIHPTVPNPYNLLSGLPPSHQWYT VLDLKDAFFCLRLHPTSQPLFAFEWRDPEMGISGQLTWTRLPQGFKNSP TLFDEALHRDLADFRIQHPDLILLQYVDDLLLAATSELDCQQGTRALLQ TLGNLGYRASAKKAQICQKQVKYLGYLLKEGQRWLTEARKETVMGQPTP KTPRQLREFLGTAGFCRLWIPGFAEMAAPLYPLTKTGTLFNWGPDQQKA YQEIKQALLTAPALGLPDLTKPFELFVDEKQGYAKGVLTQKLGPWRRPV AYLSKKLDPVAAGWPPCLRMVAAIAVLTKDAGKLTMGQPLVILAPHAVE ALVKQPPDRWLSNARMTHYQALLLDTDRVQFGPVVALNPATLLPLPEEG LQHNCLDILAEAHGTRPDLTDQPLPDADHTWYTDGSSLLQEGQRKAGAA VTTETEVIWAKALPAGTSAQRAELIALTQALKMAEGKKLNVYTDSRYAF ATAHIHGEIYRRRGLLTSEGKEIKNKDEILALLKALFLPKRLSIIHCPG HQKGHSAEARGNRMADQAARKAA Core RT (bold), annotated per above RNAseH (underlined), annotated per above

In embodiments, the gene modifying polypeptide further comprises one additional amino acid at the C-terminus of the sequence of amino acids 659-1329 of NP_057933. In embodiments, the gene modifying polypeptide comprises an RNaseH1 domain (e.g., amino acids 1178-1318 of NP_057933).

In some embodiments, a retroviral reverse transcriptase domain, e.g., M-MLV RT, may comprise one or more mutations from a wild-type sequence that may improve features of the RT, e.g., thermostability, processivity, and/or template binding. In some embodiments, an M-MLV RT domain comprises, relative to the M-MLV (WT) sequence above, one or more mutations, e.g., selected from D200N, L603W, T330P, T306K, W313F, D524G, E562Q, D583N, P51L, S67R, E67K, T197A, H204R, E302K, F309N, L435G, N454K, H594Q, D653N, R110S, K103L, e.g., a combination of mutations, such as D200N, L603W, and T330P, optionally further including T306K and W313F. In some embodiments, an M-MLV RT used herein comprises the mutations D200N, L603W, T330P, T306K and W313F. In embodiments, the mutant M-MLV RT comprises the following amino acid sequence:

M-MLV (PE2): (SEQ ID NO: 5005) TLNIEDEYRLHETSKEPDVSLGSTWLSDFPQAWAETGGMGLAVRQAPLI IPLKATSTPVSIKQYPMSQEARLGIKPHIQRLLDQGILVPCQSPWNTPL LPVKKPGTNDYRPVQDLREVNKRVEDIHPTVPNPYNLLSGLPPSHQWYT VLDLKDAFFCLRLHPTSQPLFAFEWRDPEMGISGQLTWTRLPQGFKNSP TLFNEALHRDLADFRIQHPDLILLQYVDDLLLAATSELDCQQGTRALLQ TLGNLGYRASAKKAQICQKQVKYLGYLLKEGQRWLTEARKETVMGQPTP KTPRQLREFLGKAGFCRLFIPGFAEMAAPLYPLTKPGTLFNWGPDQQKA YQEIKQALLTAPALGLPDLTKPFELFVDEKQGYAKGVLTQKLGPWRRPV AYLSKKLDPVAAGWPPCLRMVAAIAVLTKDAGKLTMGQPLVILAPHAVE ALVKQPPDRWLSNARMTHYQALLLDTDRVQFGPVVALNPATLLPLPEEG LQHNCLDILAEAHGTRPDLTDQPLPDADHTWYTDGSSLLQEGQRKAGAA VTTETEVIWAKALPAGTSAQRAELIALTQALKMAEGKKLNVYTDSRYAF ATAHIHGEIYRRRGWLTSEGKEIKNKDEILALLKALFLPKRLSIIHCPG HQKGHSAEARGNRMADQAARKAAITETPDTSTLLI

In some embodiments, a writing domain (e.g., RT domain) comprises an RNA-binding domain, e.g., that specifically binds to an RNA sequence. In some embodiments, a template RNA comprises an RNA sequence that is specifically bound by the RNA-binding domain of the writing domain.

In some embodiments, the reverse transcription domain only recognizes and reverse transcribes a specific template, e.g., a template RNA of the system. In some embodiments, the template comprises a sequence or structure that enables recognition and reverse transcription by a reverse transcription domain. In some embodiments, the template comprises a sequence or structure that enables association with an RNA-binding domain of a polypeptide component of a genome engineering system described herein. In some embodiments, the genome engineering system reverse preferably transcribes a template comprising an association sequence over a template lacking an association sequence.

The writing domain may also comprise DNA-dependent DNA polymerase activity, e.g., comprise enzymatic activity capable of writing DNA into the genome from a template DNA sequence. In some embodiments, DNA-dependent DNA polymerization is employed to complete second-strand synthesis of a target site edit. In some embodiments, the DNA-dependent DNA polymerase activity is provided by a DNA polymerase domain in the polypeptide. In some embodiments, the DNA-dependent DNA polymerase activity is provided by a reverse transcriptase domain that is also capable of DNA-dependent DNA polymerization, e.g., second-strand synthesis. In some embodiments, the DNA-dependent DNA polymerase activity is provided by a second polypeptide of the system. In some embodiments, the DNA-dependent DNA polymerase activity is provided by an endogenous host cell polymerase that is optionally recruited to the target site by a component of the genome engineering system.

In some embodiments, the reverse transcriptase domain has a lower probability of premature termination rate (P_(off)) in vitro relative to a reference reverse transcriptase domain. In some embodiments, the reference reverse transcriptase domain is a viral reverse transcriptase domain, e.g., the RT domain from M-MLV.

In some embodiments, the reverse transcriptase domain has a lower probability of premature termination rate (P_(off)) in vitro of less than about 5×10⁻³/nt, 5×10⁻⁴/nt, or 5×10⁻⁶/nt, e.g., as measured on a 1094 nt RNA. In embodiments, the in vitro premature termination rate is determined as described in Bibillo and Eickbush (2002) J Biol Chem 277(38):34836-34845 (incorporated by reference herein its entirety).

In some embodiments, the reverse transcriptase domain is able to complete at least about 30% or 50% of integrations in cells. The percent of complete integrations can be measured by dividing the number of substantially full-length integration events (e.g., genomic sites that comprise at least 98% of the expected integrated sequence) by the number of total (including substantially full-length and partial) integration events in a population of cells. In embodiments, the integrations in cells is determined (e.g., across the integration site) using long-read amplicon sequencing, e.g., as described in Karst et al. (2020) bioRxiv doi.org/10.1101/645903 (incorporated by reference herein in its entirety).

In embodiments, quantifying integrations in cells comprises counting the fraction of integrations that contain at least about 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% of the DNA sequence corresponding to the template RNA (e.g., a template RNA having a length of at least 0.05, 0.1, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 1.5, 2, 3, 4, or 5 kb, e.g., a length between 0.5-0.6, 0.6-0.7, 0.7-0.8, 0.8-0.9, 1.0-1.2, 1.2-1.4, 1.4-1.6, 1.6-1.8, 1.8-2.0, 2-3, 3-4, or 4-5 kb).

In some embodiments, the reverse transcriptase domain is capable of polymerizing dNTPs in vitro. In embodiments, the reverse transcriptase domain is capable of polymerizing dNTPs in vitro at a rate between 0.1-50 nt/sec (e.g., between 0.1-1, 1-10, or 10-50 nt/sec). In embodiments, polymerization of dNTPs by the reverse transcriptase domain is measured by a single-molecule assay, e.g., as described in Schwartz and Quake (2009) PNAS 106(48):20294-20299 (incorporated by reference in its entirety).

In some embodiments, the reverse transcriptase domain has an in vitro error rate (e.g., misincorporation of nucleotides) of between 1×10⁻³-1×10⁻⁴ or 1×10⁻⁴-1×10⁻⁵ substitutions/nt, e.g., as described in Yasukawa et al. (2017) Biochem Biophys Res Commun 492(2):147-153 (incorporated herein by reference in its entirety). In some embodiments, the reverse transcriptase domain has an error rate (e.g., misincorporation of nucleotides) in cells (e.g., HEK293T cells) of between 1×10⁻³-1×10⁻⁴ or 1×10⁻⁴-1×10⁻⁵ substitutions/nt, e.g., by long-read amplicon sequencing, e.g., as described in Karst et al. (2020) bioRxiv doi.org/10.1101/645903 (incorporated by reference herein in its entirety).

In some embodiments, the reverse transcriptase domain is capable of performing reverse transcription of a target RNA in vitro. In some embodiments, the reverse transcriptase requires a primer of at least 3 nucleotides to initiate reverse transcription of a template. In some embodiments, reverse transcription of the target RNA is determined by detection of cDNA from the target RNA (e.g., when provided with a ssDNA primer, e.g., which anneals to the target with at least 3, 4, 5, 6, 7, 8, 9, or 10 nt at the 3′ end), e.g., as described in Bibillo and Eickbush (2002) J Biol Chem 277(38):34836-34845 (incorporated herein by reference in its entirety).

In some embodiments, the reverse transcriptase domain performs reverse transcription at least 5 or 10 times more efficiently (e.g., by cDNA production), e.g., when converting its RNA template to cDNA, for example, as compared to an RNA template lacking the protein binding motif (e.g., a 3′ UTR). In embodiments, efficiency of reverse transcription is measured as described in Yasukawa et al. (2017) Biochem Biophys Res Commun 492(2):147-153 (incorporated by reference herein in its entirety).

In some embodiments, the reverse transcriptase domain specifically binds a specific RNA template with higher frequency (e.g., about 5 or 10-fold higher frequency) than any endogenous cellular RNA, e.g., when expressed in cells (e.g., HEK293T cells). In embodiments, frequency of specific binding between the reverse transcriptase domain and the template RNA are measured by CLIP-seq, e.g., as described in Lin and Miles (2019) Nucleic Acids Res 47(11):5490-5501 (incorporated herein by reference in its entirety).

Template Nucleic Acid Binding Domain

The gene modifying polypeptide typically contains regions capable of associating with the template nucleic acid (e.g., template RNA). In some embodiments, the template nucleic acid binding domain is an RNA binding domain. In some embodiments, the RNA binding domain is a modular domain that can associate with RNA molecules containing specific signatures, e.g., structural motifs. In other embodiments, the template nucleic acid binding domain (e.g., RNA binding domain) is contained within the reverse transcription domain, e.g., the reverse transcriptase-derived component has a known signature for RNA preference.

In other embodiments, the template nucleic acid binding domain (e.g., RNA binding domain) is contained within the target DNA binding domain. For example, in some embodiments, the DNA binding domain is a CRISPR-associated protein that recognizes the structure of a template nucleic acid (e.g., template RNA) comprising a gRNA. In some embodiments, a gene modifying polypeptide comprises a DNA-binding domain comprising a CRISPR-associated protein that associates with a gRNA scaffold that allows the DNA-binding domain to bind a target genomic DNA sequence. In some embodiments, the gRNA scaffold and gRNA spacer is comprised within the template nucleic acid (e.g., template RNA), thus the DNA-binding domain is also the template nucleic acid binding domain. In some embodiments, the polypeptide possesses RNA binding function in multiple domains, e.g., can bind a gRNA structure in a CRISPR-associated DNA binding domain and an additional sequence or structure in a reverse transcriptase domain.

In some embodiments, the RNA binding domain is capable of binding to a template RNA with greater affinity than a reference RNA binding domain. In some embodiments, the reference RNA binding domain is an RNA binding domain from Cas9 of S. pyogenes. In some embodiments, the RNA binding domain is capable of binding to a template RNA with an affinity between 100 pM-10 nM (e.g., between 100 pM-1 nM or 1 nM-10 nM). In some embodiments, the affinity of a RNA binding domain for its template RNA is measured in vitro, e.g., by thermophoresis, e.g., as described in Asmari et al. Methods 146:107-119 (2018) (incorporated by reference herein in its entirety). In some embodiments, the affinity of a RNA binding domain for its template RNA is measured in cells (e.g., by FRET or CLIP-Seq).

In some embodiments, the RNA binding domain is associated with the template RNA in vitro at a frequency at least about 5-fold or 10-fold higher than with a scrambled RNA. In some embodiments, the frequency of association between the RNA binding domain and the template RNA or scrambled RNA is measured by CLIP-seq, e.g., as described in Lin and Miles (2019) Nucleic Acids Res 47(11):5490-5501 (incorporated by reference herein in its entirety). In some embodiments, the RNA binding domain is associated with the template RNA in cells (e.g., in HEK293T cells) at a frequency at least about 5-fold or 10-fold higher than with a scrambled RNA. In some embodiments, the frequency of association between the RNA binding domain and the template RNA or scrambled RNA is measured by CLIP-seq, e.g., as described in Lin and Miles (2019), supra.

Endonuclease Domains and DNA Binding Domains

In some embodiments, a gene modifying polypeptide possesses the function of DNA target site cleavage via an endonuclease domain. In some embodiments, a gene modifying polypeptide comprises a DNA binding domain, e.g., for binding to a target nucleic acid. In some embodiments, a domain (e.g., a Cas domain) of the gene modifying polypeptide comprises two or more smaller domains, e.g., a DNA binding domain and an endonuclease domain. It is understood that when a DNA binding domain (e.g., a Cas domain) is said to bind to a target nucleic acid sequence, in some embodiments, the binding is mediated by a gRNA.

In some embodiments, a domain has two functions. For example, in some embodiments, the endonuclease domain is also a DNA-binding domain. In some embodiments, the endonuclease domain is also a template nucleic acid (e.g., template RNA) binding domain. For example, in some embodiments, a polypeptide comprises a CRISPR-associated endonuclease domain that binds a template RNA comprising a gRNA, binds a target DNA sequence (e.g., with complementarity to a portion of the gRNA), and cuts the target DNA sequence. In some embodiments, an endonuclease domain or endonuclease/DNA-binding domain from a heterologous source can be used or can be modified (e.g., by insertion, deletion, or substitution of one or more residues) in a gene modifying system described herein.

In some embodiments, a nucleic acid encoding the endonuclease domain or endonuclease/DNA binding domain is altered from its natural sequence to have altered codon usage, e.g. improved for human cells. In some embodiments, the endonuclease element is a heterologous endonuclease element, such as a Cas endonuclease (e.g., Cas9), a type-II restriction endonuclease (e.g., Fok1), a meganuclease (e.g., I-SceI), or other endonuclease domain.

In certain aspects, the DNA-binding domain of a gene modifying polypeptide described herein is selected, designed, or constructed for binding to a desired host DNA target sequence. In certain embodiments, the DNA-binding domain of the polypeptide is a heterologous DNA-binding element. In some embodiments the heterologous DNA binding element is a zinc-finger element or a TAL effector element, e.g., a zinc-finger or TAL polypeptide or functional fragment thereof. In some embodiments the heterologous DNA binding element is a sequence-guided DNA binding element, such as Cas9, Cpf1, or other CRISPR-related protein that has been altered to have no endonuclease activity. In some embodiments the heterologous DNA binding element retains endonuclease activity. In some embodiments, the heterologous DNA binding element retains partial endonuclease activity to cleave ssDNA, e.g., possesses nickase activity. In specific embodiments, the heterologous DNA-binding domain can be any one or more of Cas9, TAL domain, ZF domain, Myb domain, combinations thereof, or multiples thereof.

In some embodiments, DNA-binding domains are modified, for example by site-specific mutation, increasing or decreasing DNA-binding elements (for example, number and/or specificity of zinc fingers), etc., to alter DNA-binding specificity and affinity. In some embodiments a nucleic acid sequence encoding the DNA binding domain is altered from its natural sequence to have altered codon usage, e.g. improved for human cells. In embodiments, the DNA binding domain comprises one or more modifications relative to a wild-type DNA binding domain, e.g., a modification via directed evolution, e.g., phage-assisted continuous evolution (PACE).

In some embodiments, the DNA binding domain comprises a meganuclease domain (e.g., as described herein, e.g., in the endonuclease domain section), or a functional fragment thereof. In some embodiments, the meganuclease domain possesses endonuclease activity, e.g., double-strand cleavage and/or nickase activity. In other embodiments, the meganuclease domain has reduced activity, e.g., lacks endonuclease activity, e.g., the meganuclease is catalytically inactive. In some embodiments, a catalytically inactive meganuclease is used as a DNA binding domain, e.g., as described in Fonfara et al. Nucleic Acids Res 40(2):847-860 (2012), incorporated herein by reference in its entirety.

In some embodiments, a gene modifying polypeptide comprises a modification to a DNA-binding domain, e.g., relative to the wild-type polypeptide. In some embodiments, the DNA-binding domain comprises an addition, deletion, replacement, or modification to the amino acid sequence of the original DNA-binding domain. In some embodiments, the DNA-binding domain is modified to include a heterologous functional domain that binds specifically to a target nucleic acid (e.g., DNA) sequence of interest. In some embodiments, the functional domain replaces at least a portion (e.g., the entirety of) the prior DNA-binding domain of the polypeptide. In some embodiments, the functional domain comprises a zinc finger (e.g., a zinc finger that specifically binds to the target nucleic acid (e.g., DNA) sequence of interest. In some embodiments, the functional domain comprises a Cas domain (e.g., a Cas domain that specifically binds to the target nucleic acid (e.g., DNA) sequence of interest. In some embodiments, the Cas domain comprises a Cas9 or a mutant or variant thereof (e.g., as described herein). In embodiments, the Cas domain is associated with a guide RNA (gRNA), e.g., as described herein. In embodiments, the Cas domain is directed to a target nucleic acid (e.g., DNA) sequence of interest by the gRNA. In embodiments, the Cas domain is encoded in the same nucleic acid (e.g., RNA) molecule as the gRNA. In embodiments, the Cas domain is encoded in a different nucleic acid (e.g., RNA) molecule from the gRNA.

In some embodiments, the DNA binding domain is capable of binding to a target sequence (e.g., a dsDNA target sequence) with greater affinity than a reference DNA binding domain. In some embodiments, the reference DNA binding domain is a DNA binding domain from Cas9 of S. pyogenes. In some embodiments, the DNA binding domain is capable of binding to a target sequence (e.g., a dsDNA target sequence) with an affinity between 100 pM-10 nM (e.g., between 100 pM-1 nM or 1 nM-10 nM).

In some embodiments, the affinity of a DNA binding domain for its target sequence (e.g., dsDNA target sequence) is measured in vitro, e.g., by thermophoresis, e.g., as described in Asmari et al. Methods 146:107-119 (2018) (incorporated by reference herein in its entirety).

In embodiments, the DNA binding domain is capable of binding to its target sequence (e.g., dsDNA target sequence), e.g, with an affinity between 100 pM-10 nM (e.g., between 100 pM-1 nM or 1 nM-10 nM) in the presence of a molar excess of scrambled sequence competitor dsDNA, e.g., of about 100-fold molar excess.

In some embodiments, the DNA binding domain is found associated with its target sequence (e.g., dsDNA target sequence) more frequently than any other sequence in the genome of a target cell, e.g., human target cell, e.g., as measured by ChIP-seq (e.g., in HEK293T cells), e.g., as described in He and Pu (2010) Curr. Protoc Mol Biol Chapter 21 (incorporated herein by reference in its entirety). In some embodiments, the DNA binding domain is found associated with its target sequence (e.g., dsDNA target sequence) at least about 5-fold or 10-fold, more frequently than any other sequence in the genome of a target cell, e.g., as measured by ChIP-seq (e.g., in HEK293T cells), e.g., as described in He and Pu (2010), supra.

In some embodiments, the endonuclease domain has nickase activity and cleaves one strand of a target DNA. In some embodiments, nickase activity reduces the formation of double-stranded breaks at the target site. In some embodiments, the endonuclease domain creates a staggered nick structure in the first and second strands of a target DNA. In some embodiments, a staggered nick structure generates free 3′ overhangs at the target site. In some embodiments, free 3′ overhangs at the target site improve editing efficiency, e.g., by enhancing access and annealing of a 3′ homology region of a template nucleic acid. In some embodiments, a staggered nick structure reduces the formation of double-stranded breaks at the target site.

In some embodiments, the endonuclease domain cleaves both strands of a target DNA, e.g., results in blunt-end cleavage of a target with no ssDNA overhangs on either side of the cut-site. The amino acid sequence of an endonuclease domain of a gene modifying system described herein may be at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99% identical to the amino acid sequence of an endonuclease domain described herein, e.g., an endonuclease domain as described herein.

In certain embodiments, the heterologous endonuclease is Fok1 or a functional fragment thereof. In certain embodiments, the heterologous endonuclease is a Holliday junction resolvase or homolog thereof, such as the Holliday junction resolving enzyme from Sulfolobus solfataricus—Ssol Hje (Govindaraju et al., Nucleic Acids Research 44:7, 2016). In certain embodiments, the heterologous endonuclease is the endonuclease of the large fragment of a spliceosomal protein, such as Prp8 (Mahbub et al., Mobile DNA 8:16, 2017). In certain embodiments, the heterologous endonuclease is derived from a CRISPR-associated protein, e.g., Cas9. In certain embodiments, the heterologous endonuclease is engineered to have only ssDNA cleavage activity, e.g., only nickase activity, e.g., be a Cas9 nickase, e.g., SpCas9 with D10A, H840A, or N863A mutations. Table 8 provides exemplary Cas proteins and mutations associated with nickase activity. In still other embodiments, homologous endonuclease domains are modified, for example by site-specific mutation, to alter DNA endonuclease activity. In still other embodiments, endonuclease domains are modified to reduce DNA-sequence specificity, e.g., by truncation to remove domains that confer DNA-sequence specificity or mutation to inactivate regions conferring DNA-sequence specificity.

In some embodiments, the endonuclease domain has nickase activity and does not form double-stranded breaks. In some embodiments, the endonuclease domain forms single-stranded breaks at a higher frequency than double-stranded breaks, e.g., at least 90%, 95%, 96%, 97%, 98%, or 99% of the breaks are single-stranded breaks, or less than 10%, 5%, 4%, 3%, 2%, or 1% of the breaks are double-stranded breaks. In some embodiments, the endonuclease forms substantially no double-stranded breaks. In some embodiments, the endonuclease does not form detectable levels of double-stranded breaks.

In some embodiments, the endonuclease domain has nickase activity that nicks the target site DNA of the first strand; e.g., in some embodiments, the endonuclease domain cuts the genomic DNA of the target site near to the site of alteration on the strand that will be extended by the writing domain. In some embodiments, the endonuclease domain has nickase activity that nicks the target site DNA of the first strand and does not nick the target site DNA of the second strand. For example, when a polypeptide comprises a CRISPR-associated endonuclease domain having nickase activity, in some embodiments, said CRISPR-associated endonuclease domain nicks the target site DNA strand containing the PAM site (e.g., and does not nick the target site DNA strand that does not contain the PAM site). As a further example, when a polypeptide comprises a CRISPR-associated endonuclease domain having nickase activity, in some embodiments, said CRISPR-associated endonuclease domain nicks the target site DNA strand not containing the PAM site (e.g., and does not nick the target site DNA strand that contains the PAM site).

In some other embodiments, the endonuclease domain has nickase activity that nicks the target site DNA of the first strand and the second strand. Without wishing to be bound by theory, after a writing domain (e.g., RT domain) of a polypeptide described herein polymerizes (e.g., reverse transcribes) from the heterologous object sequence of a template nucleic acid (e.g., template RNA), the cellular DNA repair machinery must repair the nick on the first DNA strand. The target site DNA now contains two different sequences for the first DNA strand: one corresponding to the original genomic DNA (e.g., having a free 5′ end) and a second corresponding to that polymerized from the heterologous object sequence (e.g., having a free 3′ end). It is thought that the two different sequences equilibrate with one another, first one hybridizing the second strand, then the other, and which sequence the cellular DNA repair apparatus incorporates into its repaired target site may be a stochastic process. Without wishing to be bound by theory, it is thought that introducing an additional nick to the second-strand may bias the cellular DNA repair machinery to adopt the heterologous object sequence-based sequence more frequently than the original genomic sequence (Anzalone et al. Nature 576:149-157 (2019)). In some embodiments, the additional nick is positioned at least 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 115, 120, 125, 130, 135, 140, 145, or 150 nucleotides 5′ or 3′ of the target site modification (e.g., the insertion, deletion, or substitution) or to the nick on the first strand.

Alternatively, or additionally, without wishing to be bound by theory, it is thought that an additional nick to the second strand may promote second-strand synthesis. In some embodiments, where the gene modifying system has inserted or substituted a portion of the first strand, synthesis of a new sequence corresponding to the insertion/substitution in the second strand is necessary.

In some embodiments, the polypeptide comprises a single domain having endonuclease activity (e.g., a single endonuclease domain) and said domain nicks both the first strand and the second strand. For example, in such an embodiment the endonuclease domain may be a CRISPR-associated endonuclease domain, and the template nucleic acid (e.g., template RNA) comprises a gRNA spacer that directs nicking of the first strand and an additional gRNA spacer that directs nicking of the second strand. In some embodiments, the polypeptide comprises a plurality of domains having endonuclease activity, and a first endonuclease domain nicks the first strand and a second endonuclease domain nicks the second strand (optionally, the first endonuclease domain does not (e.g., cannot) nick the second strand and the second endonuclease domain does not (e.g., cannot) nick the first strand).

In some embodiments, the endonuclease domain is capable of nicking a first strand and a second strand. In some embodiments, the first and second strand nicks occur at the same position in the target site but on opposite strands. In some embodiments, the second strand nick occurs in a staggered location, e.g., upstream or downstream, from the first nick. In some embodiments, the endonuclease domain generates a target site deletion if the second strand nick is upstream of the first strand nick. In some embodiments, the endonuclease domain generates a target site duplication if the second strand nick is downstream of the first strand nick. In some embodiments, the endonuclease domain generates no duplication and/or deletion if the first and second strand nicks occur in the same position of the target site. In some embodiments, the endonuclease domain has altered activity depending on protein conformation or RNA-binding status, e.g., which promotes the nicking of the first or second strand (e.g., as described in Christensen et al. PNAS 2006; incorporated by reference herein in its entirety).

In some embodiments, the endonuclease domain comprises a meganuclease, or a functional fragment thereof. In some embodiments, the endonuclease domain comprises a homing endonuclease, or a functional fragment thereof. In some embodiments, the endonuclease domain comprises a meganuclease from the LAGLIDADG (SEQ ID NO: 15464), GIY-YIG, HNH, His-Cys Box, or PD-(D/E) XK families, or a functional fragment or variant thereof, e.g., which possess conserved amino acid motifs, e.g., as indicated in the family names. In some embodiments, the endonuclease domain comprises a meganuclease, or fragment thereof, chosen from, e.g., I-SmaMI (Uniprot F7WD42), I-SceI (Uniprot P03882), I-Anil (Uniprot P03880), I-DmoI (Uniprot P21505), I-CreI (Uniprot P05725), I-TevI (Uniprot P13299), I-OnuI (Uniprot Q4VWW5), or I-BmoI (Uniprot Q9ANR6). In some embodiments, the meganuclease is naturally monomeric, e.g., I-SceI, I-TevI, or dimeric, e.g., I-CreI, in its functional form. For example, the LAGLIDADG meganucleases (“LAGLIDADG” disclosed as SEQ ID NO: 15464) with a single copy of the LAGLIDADG motif (SEQ ID NO: 15464) generally form homodimers, whereas members with two copies of the LAGLIDADG motif (SEQ ID NO: 15464) are generally found as monomers. In some embodiments, a meganuclease that normally forms as a dimer is expressed as a fusion, e.g., the two subunits are expressed as a single ORF and, optionally, connected by a linker, e.g., an I-CreI dimer fusion (Rodriguez-Fornes et al. Gene Therapy 2020; incorporated by reference herein in its entirety). In some embodiments, a meganuclease, or a functional fragment thereof, is altered to favor nickase activity for one strand of a double-stranded DNA molecule, e.g., I-SceI (K1221 and/or K2231) (Niu et al. J Mol Biol 2008), I-Anil (K227M) (McConnell Smith et al. PNAS 2009), I-DmoI (Q42A and/or K120M) (Molina et al. J Biol Chem 2015). In some embodiments, a meganuclease or functional fragment thereof possessing this preference for single-strand cleavage is used as an endonuclease domain, e.g., with nickase activity. In some embodiments, an endonuclease domain comprises a meganuclease, or a functional fragment thereof, which naturally targets or is engineered to target a safe harbor site, e.g., an I-CreI targeting SH6 site (Rodriguez-Fornes et al., supra). In some embodiments, an endonuclease domain comprises a meganuclease, or a functional fragment thereof, with a sequence tolerant catalytic domain, e.g., I-TevI recognizing the minimal motif CNNNG (Kleinstiver et al. PNAS 2012). In some embodiments, a target sequence tolerant catalytic domain is fused to a DNA binding domain, e.g., to direct activity, e.g., by fusing I-TevI to: (i) zinc fingers to create Tev-ZFEs (Kleinstiver et al. PNAS 2012), (ii) other meganucleases to create MegaTevs (Wolfs et al. Nucleic Acids Res 2014), and/or (iii) Cas9 to create TevCas9 (Wolfs et al. PNAS 2016).

In some embodiments, the endonuclease domain comprises a restriction enzyme, e.g., a Type IIS or Type IIP restriction enzyme. In some embodiments, the endonuclease domain comprises a Type IIS restriction enzyme, e.g., FokI, or a fragment or variant thereof. In some embodiments, the endonuclease domain comprises a Type IIP restriction enzyme, e.g., PvuII, or a fragment or variant thereof. In some embodiments, a dimeric restriction enzyme is expressed as a fusion such that it functions as a single chain, e.g., a FokI dimer fusion (Minczuk et al. Nucleic Acids Res 36(12):3926-3938 (2008)).

The use of additional endonuclease domains is described, for example, in Guha and Edgell Int J Mol Sci 18(22):2565 (2017), which is incorporated herein by reference in its entirety.

In some embodiments, a gene modifying polypeptide comprises a modification to an endonuclease domain, e.g., relative to a wild-type Cas protein. In some embodiments, the endonuclease domain comprises an addition, deletion, replacement, or modification to the amino acid sequence of the wild-type Cas protein. In some embodiments, the endonuclease domain is modified to include a heterologous functional domain that binds specifically to and/or induces endonuclease cleavage of a target nucleic acid (e.g., DNA) sequence of interest. In some embodiments, the endonuclease domain comprises a zinc finger. In embodiments, the endonuclease domain comprising the Cas domain is associated with a guide RNA (gRNA), e.g., as described herein. In some embodiments, the endonuclease domain is modified to include a functional domain that does not target a specific target nucleic acid (e.g., DNA) sequence. In embodiments, the endonuclease domain comprises a FokI domain.

In some embodiments, the endonuclease domain is associated with the target dsDNA in vitro at a frequency at least about 5-fold or 10-fold higher than with a scrambled dsDNA. In some embodiments, the endonuclease domain is associated with the target dsDNA in vitro at a frequency at least about 5-fold or 10-fold higher than with a scrambled dsDNA, e.g., in a cell (e.g., a HEK293T cell). In some embodiments, the frequency of association between the endonuclease domain and the target DNA or scrambled DNA is measured by ChIP-seq, e.g., as described in He and Pu (2010) Curr. Protoc Mol Biol Chapter 21 (incorporated by reference herein in its entirety).

In some embodiments, the endonuclease domain can catalyze the formation of a nick at a target sequence, e.g., to an increase of at least about 5-fold or 10-fold relative to a non-target sequence (e.g., relative to any other genomic sequence in the genome of the target cell). In some embodiments, the level of nick formation is determined using NickSeq, e.g., as described in Elacqua et al. (2019) bioRxiv doi.org/10.1101/867937 (incorporated herein by reference in its entirety).

In some embodiments, the endonuclease domain is capable of nicking DNA in vitro. In embodiments, the nick results in an exposed base. In embodiments, the exposed base can be detected using a nuclease sensitivity assay, e.g., as described in Chaudhry and Weinfeld (1995) Nucleic Acids Res 23(19):3805-3809 (incorporated by reference herein in its entirety). In embodiments, the level of exposed bases (e.g., detected by the nuclease sensitivity assay) is increased by at least 10%, 50%, or more relative to a reference endonuclease domain. In some embodiments, the reference endonuclease domain is an endonuclease domain from Cas9 of S. pyogenes.

In some embodiments, the endonuclease domain is capable of nicking DNA in a cell. In embodiments, the endonuclease domain is capable of nicking DNA in a HEK293T cell. In embodiments, an unrepaired nick that undergoes replication in the absence of Rad51 results in increased NHEJ rates at the site of the nick, which can be detected, e.g., by using a Rad51 inhibition assay, e.g., as described in Bothmer et al. (2017) Nat Commun 8:13905 (incorporated by reference herein in its entirety). In embodiments, NHEJ rates are increased above 0-5%. In embodiments, NHEJ rates are increased to 20-70% (e.g., between 30%-60% or 40-50%), e.g., upon Rad51 inhibition.

In some embodiments, the endonuclease domain releases the target after cleavage. In some embodiments, release of the target is indicated indirectly by assessing for multiple turnovers by the enzyme, e.g., as described in Yourik at al. RNA 25(1):35-44 (2019) (incorporated herein by reference in its entirety) and shown in FIG. 2 . In some embodiments, the k_(exp) of an endonuclease domain is 1×10⁻³-1×10⁻⁵ min-1 as measured by such methods.

In some embodiments, the endonuclease domain has a catalytic efficiency (k_(cat)/K_(m)) greater than about 1×10⁸ s⁻¹ M⁻¹ in vitro. In embodiments, the endonuclease domain has a catalytic efficiency greater than about 1×10⁵, 1×10⁶, 1×10⁷, or 1×10⁸, s⁻¹ M⁻¹ in vitro. In embodiments, catalytic efficiency is determined as described in Chen et al. (2018) Science 360(6387):436-439 (incorporated herein by reference in its entirety). In some embodiments, the endonuclease domain has a catalytic efficiency (k_(cat)/K_(m)) greater than about 1×10⁸ s⁻¹ M⁻¹ in cells. In embodiments, the endonuclease domain has a catalytic efficiency greater than about 1×10⁵, 1×10⁶, 1×10⁷, or 1×10⁸ s⁻¹ M⁻¹ in cells.

Gene Modifying Polypeptides Comprising Cas Domains

In some embodiments, a gene modifying polypeptide described herein comprises a Cas domain. In some embodiments, the Cas domain can direct the gene modifying polypeptide to a target site specified by a gRNA spacer, thereby modifying a target nucleic acid sequence in “cis”. In some embodiments, a gene modifying polypeptide is fused to a Cas domain. In some embodiments, a gene modifying polypeptide comprises a CRISPR/Cas domain (also referred to herein as a CRISPR-associated protein). In some embodiments, a CRISPR/Cas domain comprises a protein involved in the clustered regulatory interspaced short palindromic repeat (CRISPR) system, e.g., a Cas protein, and optionally binds a guide RNA, e.g., single guide RNA (sgRNA).

CRISPR systems are adaptive defense systems originally discovered in bacteria and archaea. CRISPR systems use RNA-guided nucleases termed CRISPR-associated or “Cas” endonucleases (e.g., Cas9 or Cpf1) to cleave foreign DNA. For example, in a typical CRISPR-Cas system, an endonuclease is directed to a target nucleotide sequence (e.g., a site in the genome that is to be sequence-edited) by sequence-specific, non-coding “guide RNAs” that target single- or double-stranded DNA sequences. Three classes (I-III) of CRISPR systems have been identified. The class II CRISPR systems use a single Cas endonuclease (rather than multiple Cas proteins). One class II CRISPR system includes a type II Cas endonuclease such as Cas9, a CRISPR RNA (“crRNA”), and a trans-activating crRNA (“tracrRNA”). The crRNA contains a “spacer” sequence, a typically about 20-nucleotide RNA sequence that corresponds to a target DNA sequence (“protospacer”). In the wild-type system, and in some engineered systems, crRNA also contains a region that binds to the tracrRNA to form a partially double-stranded structure that is cleaved by RNase III, resulting in a crRNA/tracrRNA hybrid molecule. A crRNA/tracrRNA hybrid then directs the Cas endonuclease to recognize and cleave a target DNA sequence. A target DNA sequence is generally adjacent to a “protospacer adjacent motif” (“PAM”) that is specific for a given Cas endonuclease and required for cleavage activity at a target site matching the spacer of the crRNA. CRISPR endonucleases identified from various prokaryotic species have unique PAM sequence requirements, e.g., as listed for exemplary Cas enzymes in Table 7; examples of PAM sequences include 5′-NGG (Streptococcus pyogenes), 5′-NNAGAA (Streptococcus thermophilus CRISPR1), 5′-NGGNG (Streptococcus thermophilus CRISPR3), and 5′-NNNGATT (Neisseria meningitidis). Some endonucleases, e.g., Cas9 endonucleases, are associated with G-rich PAM sites, e.g., 5′-NGG, and perform blunt-end cleaving of the target DNA at a location 3 nucleotides upstream from (5′ from) the PAM site. Another class II CRISPR system includes the type V endonuclease Cpf1, which is smaller than Cas9; examples include AsCpf1 (from Acidaminococcus sp.) and LbCpf1 (from Lachnospiraceae sp.). Cpf1-associated CRISPR arrays are processed into mature crRNAs without the requirement of a tracrRNA; in other words, a Cpf1 system, in some embodiments, comprises only Cpf1 nuclease and a crRNA to cleave a target DNA sequence. Cpf1 endonucleases, are typically associated with T-rich PAM sites, e.g., 5′-TTN. Cpf1 can also recognize a 5′-CTA PAM motif. Cpf1 typically cleaves a target DNA by introducing an offset or staggered double-strand break with a 4- or 5-nucleotide 5′ overhang, for example, cleaving a target DNA with a 5-nucleotide offset or staggered cut located 18 nucleotides downstream from (3′ from) from a PAM site on the coding strand and 23 nucleotides downstream from the PAM site on the complimentary strand; the 5-nucleotide overhang that results from such offset cleavage allows more precise genome editing by DNA insertion by homologous recombination than by insertion at blunt-end cleaved DNA. See, e.g., Zetsche et al. (2015) Cell, 163:759-771.

A variety of CRISPR associated (Cas) genes or proteins can be used in the technologies provided by the present disclosure and the choice of Cas protein will depend upon the particular conditions of the method. Specific examples of Cas proteins include class II systems including Cas1, Cas2, Cas3, Cas4, Cas5, Cas6, Cas7, Cas8, Cas9, Cas10, Cpf1, C2C1, or C2C3. In some embodiments, a Cas protein, e.g., a Cas9 protein, may be from any of a variety of prokaryotic species. In some embodiments a particular Cas protein, e.g., a particular Cas9 protein, is selected to recognize a particular protospacer-adjacent motif (PAM) sequence. In some embodiments, a DNA-binding domain or endonuclease domain includes a sequence targeting polypeptide, such as a Cas protein, e.g., Cas9. In certain embodiments a Cas protein, e.g., a Cas9 protein, may be obtained from a bacteria or archaea or synthesized using known methods. In certain embodiments, a Cas protein may be from a gram-positive bacteria or a gram-negative bacteria. In certain embodiments, a Cas protein may be from a Streptococcus (e.g., a S. pyogenes, or a S. thermophilus), a Francisella (e.g., an F. novicida), a Staphylococcus (e.g., an S. aureus), an Acidaminococcus (e.g., an Acidaminococcus sp. BV3L6), a Neisseria (e.g., an N. meningitidis), a Cryptococcus, a Corynebacterium, a Haemophilus, a Eubacterium, a Pasteurella, a Prevotella, a Veillonella, or a Marinobacter.

In some embodiments, a gene modifying polypeptide may comprise the amino acid sequence of SEQ ID NO: 4000 below, or a sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% identity thereto. In embodiments, the amino acid sequence of SEQ ID NO: 4000 below, or the sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% identity thereto, is positioned at the N-terminal end of the gene modifying polypeptide. In embodiments, the amino acid sequence of SEQ ID NO: 4000 below, or the sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% identity thereto, is positioned within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, or 30 amino acids of the N-terminal end of the gene modifying polypeptide.

Exemplary N-Terminal NLS-Cas9 Domain

(SEQ ID NO: 4000) MPAAKRVKLDGGDKKYSIGLDIGTNSVGWAVITDEYKVPSKKFKVLGNT DRHSIKKNLIGALLFDSGETAEATRLKRTARRRYTRRKNRICYLQEIFS NEMAKVDDSFFHRLEESFLVEEDKKHERHPIFGNIVDEVAYHEKYPTIY HLRKKLVDSTDKADLRLIYLALAHMIKFRGHFLIEGDLNPDNSDVDKLF IQLVQTYNQLFEENPINASGVDAKAILSARLSKSRRLENLIAQLPGEKK NGLFGNLIALSLGLTPNFKSNFDLAEDAKLQLSKDTYDDDLDNLLAQIG DQYADLFLAAKNLSDAILLSDILRVNTEITKAPLSASMIKRYDEHHQDL TLLKALVRQQLPEKYKEIFFDQSKNGYAGYIDGGASQEEFYKFIKPILE KMDGTEELLVKLNREDLLRKQRTFDNGSIPHQIHLGELHAILRRQEDFY PFLKDNREKIEKILTFRIPYYVGPLARGNSRFAWMTRKSEETITPWNFE EVVDKGASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYFTVYNELTKVK YVTEGMRKPAFLSGEQKKAIVDLLFKTNRKVTVKQLKEDYFKKIECFDS VEISGVEDRFNASLGTYHDLLKIIKDKDFLDNEENEDILEDIVLTLTLF EDREMIEERLKTYAHLFDDKVMKQLKRRRYTGWGRLSRKLINGIRDKQS GKTILDFLKSDGFANRNFMQLIHDDSLTFKEDIQKAQVSGQGDSLHEHI ANLAGSPAIKKGILQTVKVVDELVKVMGRHKPENIVIEMARENQTTQKG QKNSRERMKRIEEGIKELGSQILKEHPVENTQLQNEKLYLYYLQNGRDM YVDQELDINRLSDYDVDHIVPQSFLKDDSIDNKVLTRSDKARGKSDNVP SEEVVKKMKNYWRQLLNAKLITQRKFDNLTKAERGGLSELDKAGFIKRQ LVETRQITKHVAQILDSRMNTKYDENDKLIREVKVITLKSKLVSDFRKD FQFYKVREINNYHHAHDAYLNAVVGTALIKKYPKLESEFVYGDYKVYDV RKMIAKSEQEIGKATAKYFFYSNIMNFFKTEITLANGEIRKRPLIETNG ETGEIVWDKGRDFATVRKVLSMPQVNIVKKTEVQTGGFSKESILPKRNS DKLIARKKDWDPKKYGGFDSPTVAYSVLVVAKVEKGKSKKLKSVKELLG ITIMERSSFEKNPIDFLEAKGYKEVKKDLIIKLPKYSLFELENGRKRML ASAGELQKGNELALPSKYVNFLYLASHYEKLKGSPEDNEQKQLFVEQHK HYLDEIIEQISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENIIHL FTLTNLGAPAAFKYFDTTIDRKRYTSTKEVLDATLIHQSITGLYETRID LSQLGGDGG

In some embodiments, a gene modifying polypeptide may comprise the amino acid sequence of SEQ ID NO: 4001 below, or a sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% identity thereto. In embodiments, the amino acid sequence of SEQ ID NO: 4001 below, or the sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% identity thereto, is positioned at the C-terminal end of the gene modifying polypeptide. In embodiments, the amino acid sequence of SEQ ID NO: 4001 below, or the sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% identity thereto, is positioned within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, or 30 amino acids of the C-terminal end of the gene modifying polypeptide.

Exemplary C-Terminal Sequence Comprising an NLS

(SEQ ID NO: 4001) AGKRTADGSEFEKRTADGSEFESPKKKAKVE

Exemplary Benchmarking Sequence

(SEQ ID NO: 4002) MPAAKRVKLDGGDKKYSIGLDIGTNSVGWAVITDEYKVPSKKFKVLGNT DRHSIKKNLIGALLFDSGETAEATRLKRTARRRYTRRKNRICYLQEIFS NEMAKVDDSFFHRLEESFLVEEDKKHERHPIFGNIVDEVAYHEKYPTIY HLRKKLVDSTDKADLRLIYLALAHMIKFRGHFLIEGDLNPDNSDVDKLF IQLVQTYNQLFEENPINASGVDAKAILSARLSKSRRLENLIAQLPGEKK NGLFGNLIALSLGLTPNFKSNFDLAEDAKLQLSKDTYDDDLDNLLAQIG DQYADLFLAAKNLSDAILLSDILRVNTEITKAPLSASMIKRYDEHHQDL TLLKALVRQQLPEKYKEIFFDQSKNGYAGYIDGGASQEEFYKFIKPILE KMDGTEELLVKLNREDLLRKQRTFDNGSIPHQIHLGELHAILRRQEDFY PFLKDNREKIEKILTFRIPYYVGPLARGNSRFAWMTRKSEETITPWNFE EVVDKGASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYFTVYNELTKVK YVTEGMRKPAFLSGEQKKAIVDLLFKTNRKVTVKQLKEDYFKKIECFDS VEISGVEDRFNASLGTYHDLLKIIKDKDFLDNEENEDILEDIVLTLTLF EDREMIEERLKTYAHLFDDKVMKQLKRRRYTGWGRLSRKLINGIRDKQS GKTILDFLKSDGFANRNFMQLIHDDSLTFKEDIQKAQVSGQGDSLHEHI ANLAGSPAIKKGILQTVKVVDELVKVMGRHKPENIVIEMARENQTTQKG QKNSRERMKRIEEGIKELGSQILKEHPVENTQLQNEKLYLYYLQNGRDM YVDQELDINRLSDYDVDHIVPQSFLKDDSIDNKVLTRSDKARGKSDNVP SEEVVKKMKNYWRQLLNAKLITQRKFDNLTKAERGGLSELDKAGFIKRQ LVETRQITKHVAQILDSRMNTKYDENDKLIREVKVITLKSKLVSDFRKD FQFYKVREINNYHHAHDAYLNAVVGTALIKKYPKLESEFVYGDYKVYDV RKMIAKSEQEIGKATAKYFFYSNIMNFFKTEITLANGEIRKRPLIETNG ETGEIVWDKGRDFATVRKVLSMPQVNIVKKTEVQTGGFSKESILPKRNS DKLIARKKDWDPKKYGGFDSPTVAYSVLVVAKVEKGKSKKLKSVKELLG ITIMERSSFEKNPIDFLEAKGYKEVKKDLIIKLPKYSLFELENGRKRML ASAGELQKGNELALPSKYVNFLYLASHYEKLKGSPEDNEQKQLFVEQHK HYLDEIIEQISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENIIHL FTLTNLGAPAAFKYFDTTIDRKRYTSTKEVLDATLIHQSITGLYETRID LSQLGGDGGSGGSSGGSSGSETPGTSESATPESSGGSSGGSSGGTLNIE DEYRLHETSKEPDVSLGSTWLSDFPQAWAETGGMGLAVRQAPLIIPLKA TSTPVSIKQYPMSQEARLGIKPHIQRLLDQGILVPCQSPWNTPLLPVKK PGTNDYRPVQDLREVNKRVEDIHPTVPNPYNLLSGLPPSHQWYTVLDLK DAFFCLRLHPTSQPLFAFEWRDPEMGISGQLTWTRLPQGFKNSPTLFNE ALHRDLADFRIQHPDLILLQYVDDLLLAATSELDCQQGTRALLQTLGNL GYRASAKKAQICQKQVKYLGYLLKEGQRWLTEARKETVMGQPTPKTPRQ LREFLGKAGFCRLFIPGFAEMAAPLYPLTKPGTLFNWGPDQQKAYQEIK QALLTAPALGLPDLTKPFELFVDEKQGYAKGVLTQKLGPWRRPVAYLSK KLDPVAAGWPPCLRMVAAIAVLTKDAGKLTMGQPLVILAPHAVEALVKQ PPDRWLSNARMTHYQALLLDTDRVQFGPVVALNPATLLPLPEEGLQHNC LDILAEAHGTRPDLTDQPLPDADHTWYTDGSSLLQEGQRKAGAAVTTET EVIWAKALPAGTSAQRAELIALTQALKMAEGKKLNVYTDSRYAFATAHI HGEIYRRRGWLTSEGKEIKNKDEILALLKALFLPKRLSIIHCPGHQKGH SAEARGNRMADQAARKAAITETPDTSTLLIENSSPSGGSKRTADGSEFE AGKRTADGSEFEKRTADGSEFESPKKKAKVE

In some embodiments, a gene modifying polypeptide may comprise a Cas domain as listed in Table 7 or 8, or a functional fragment thereof, or a sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% identity thereto.

TABLE 7 CRISPR/Cas Proteins, Species, and Mutations # of Mutations to alter PAM Mutations to make Name Enzyme Species AAs PAM recognition catalytically dead FnCas9 Cas9 Francisella 1629 5′-NGG-3′ Wt D11A/H969A/N995A novicida FnCas9 Cas9 Francisella 1629 5′-YG-3′ E1369R/E1449H/R1556A D11A/H969A/N995A RHA novicida SaCas9 Cas9 Staphylococcus 1053 5′-NNGRRT- Wt D10A/H557A aureus 3′ SaCas9 Cas9 Staphylococcus 1053 5′-NNNRRT- E782K/N968K/R1015H D10A/H557A KKH aureus 3′ SpCas9 Cas9 Streptococcus 1368 5′-NGG-3′ Wt D10A/D839A/H840A/ pyogenes N863A SpCas9 Cas9 Streptococcus 1368 5′-NGA-3′ D1135V/R1335Q/T1337R D10A/D839A/H840A/ VQR pyogenes N863A AsCpf1 Cpf1 Acidaminococcus 1307 5′-TYCV-3′ S542R/K607R E993A RR sp. BV3L6 AsCpf1 Cpf1 Acidaminococcus 1307 5′-TATV-3′ S542R/K548V/N552R E993A RVR sp. BV3L6 FnCpf1 Cpf1 Francisella 1300 5′-NTTN-3′ Wt D917A/E1006A/D1255A novicida NmCas9 Cas9 Neisseria 1082 5′- Wt D16A/D587A/H588A/ meningitidis NNNGATT- N611A 3′

TABLE 8 Amino Acid Sequences of CRISPR/Cas Proteins, Species, and Mutations Nickase Nickase Nickase Variant Parental Host(s) Protein Sequence SEQ ID NO: (HNH) (HNH) (RuvC) Nme2Cas9 Neisseria meningitidis MAAFKPNPINYILGLDIGIASVGWAMVEIDEEENPIRLIDLGVRVFERAEVPK 9,001 N611A H588A D16A TGDSLAMARRLARSVRRLTRRRAHRLLRARRLLKREGVLQAADFDENGLIKS LPNTPWQLRAAALDRKLTPLEWSAVLLHLIKHRGYLSQRKNEGETADKELG ALLKGVANNAHALQTGDFRTPAELALNKFEKESGHIRNQRGDYSHTFSRKD LQAELILLFEKQKEFGNPHVSGGLKEGIETLLMTQRPALSGDAVQKMLGHCT FEPAEPKAAKNTYTAERFIWLTKLNNLRILEQGSERPLTDTERATLMDEPYRK SKLTYAQARKLLGLEDTAFFKGLRYGKDNAEASTLMEMKAYHAISRALEKEG LKDKKSPLNLSSELQDEIGTAFSLFKTDEDITGRLKDRVQPEILEALLKHISFDKF VQISLKALRRIVPLMEQGKRYDEACAEIYGDHYGKKNTEEKIYLPPIPADEIRN PVVLRALSQARKVINGVVRRYGSPARIHIETAREVGKSFKDRKEIEKRQEENR KDREKAAAKFREYFPNFVGEPKSKDILKLRLYEQQHGKCLYSGKEINLVRLNE KGYVEIDHALPFSRTWDDSFNNKVLVLGSENQNKGNQTPYEYFNGKDNSR EWQEFKARVETSRFPRSKKQRILLQKFDEDGFKECNLNDTRYVNRFLCQFVA DHILLTGKGKRRVFASNGQITNLLRGFWGLRKVRAENDRHHALDAVVVACS TVAMQQKITRFVRYKEMNAFDGKTIDKETGKVLHQKTHFPQPWEFFAQEV MIRVFGKPDGKPEFEEADTPEKLRTLLAEKLSSRPEAVHEYVTPLFVSRAPNR KMSGAHKDTLRSAKRFVKHNEKISVKRVWLTEIKLADLENMVNYKNGREIEL YEALKARLEAYGGNAKQAFDPKDNPFYKKGGQLVKAVRVEKTQESGVLLNK KNAYTIADNGDMVRVDVFCKVDKKGKNQYFIVPIYAWQVAENILPDIDCKG YRIDDSYTFCFSLHKYDLIAFQKDEKSKVEFAYYINCDSSNGRFYLAWHDKGS KEQQFRISTQNLVLIQKYQVNELGKEIRPCRLKKRPPVR PpnCas9 Pasteurella pneumotropica MQNNPLNYILGLDLGIASIGWAVVEIDEESSPIRLIDVGVRTFERAEVAKTGE 9,002 N605A H582A D13A SLALSRRLARSSRRLIKRRAERLKKAKRLLKAEKILHSIDEKLPINVWQLRVKGL KEKLERQEWAAVLLHLSKHRGYLSQRKNEGKSDNKELGALLSGIASNHQML QSSEYRTPAEIAVKKFQVEEGHIRNQRGSYTHTFSRLDLLAEMELLFQRQAEL GNSYTSTTLLENLTALLMWQKPALAGDAILKMLGKCTFEPSEYKAAKNSYSA ERFVWLTKLNNLRILENGTERALNDNERFALLEQPYEKSKLTYAQVRAMLAL SDNAIFKGVRYLGEDKKTVESKTTLIEMKFYHQIRKTLGSAELKKEWNELKGN SDLLDEIGTAFSLYKTDDDICRYLEGKLPERVLNALLENLNFDKFIQLSLKALHQ ILPLMLQGQRYDEAVSAIYGDHYGKKSTETTRLLPTIPADEIRNPVVLRTLTQA RKVINAVVRLYGSPARIHIETAREVGKSYQDRKKLEKQQEDNRKQRESAVKK FKEMFPHFVGEPKGKDILKMRLYELQQAKCLYSGKSLELHRLLEKGYVEVDH ALPFSRTWDDSFNNKVLVLANENQNKGNLTPYEWLDGKNNSERWQHFVV RVQTSGFSYAKKQRILNHKLDEKGFIERNLNDTRYVARFLCNFIADNMLLVG KGKRNVFASNGQITALLRHRWGLQKVREQNDRHHALDAVVVACSTVAMQ QKITRFVRYNEGNVFSGERIDRETGEIIPLHFPSPWAFFKENVEIRIFSENPKLE LENRLPDYPQYNHEWVQPLFVSRMPTRKMTGQGHMETVKSAKRLNEGLS VLKVPLTQLKLSDLERMVNRDREIALYESLKARLEQFGNDPAKAFAEPFYKKG GALVKAVRLEQTQKSGVLVRDGNGVADNASMVRVDVFTKGGKYFLVPIYT WQVAKGILPNRAATQGKDENDWDIMDEMATFQFSLCQNDLIKLVTKKKTI FGYFNGLNRATSNINIKEHDLDKSKGKLGIYLEVGVKLAISLEKYQVDELGKNI RPCRPTKRQHVR SauCas9 Staphylococcus aureus MKRNYILGLDIGITSVGYGIIDYETRDVIDAGVRLFKEANVENNEGRRSKRGA 9,003 N580A H557A D10A RRLKRRRRHRIQRVKKLLFDYNLLTDHSELSGINPYEARVKGLSQKLSEEEFSA ALLHLAKRRGVHNVNEVEEDTGNELSTKEQISRNSKALEEKYVAELQLERLKK DGEVRGSINRFKTSDYVKEAKQLLKVQKAYHQLDQSFIDTYIDLLETRRTYYE GPGEGSPFGWKDIKEWYEMLMGHCTYFPEELRSVKYAYNADLYNALNDLN NLVITRDENEKLEYYEKFQIIENVFKQKKKPTLKQIAKEILVNEEDIKGYRVTST GKPEFTNLKVYHDIKDITARKEIIENAELLDQIAKILTIYQSSEDIQEELTNLNSE LTQEEIEQISNLKGYTGTHNLSLKAINLILDELWHTNDNQIAIFNRLKLVPKKV DLSQQKEIPTTLVDDFILSPVVKRSFIQSIKVINAIIKKYGLPNDIIIELAREKNSK DAQKMINEMQKRNRQTNERIEEIIRTTGKENAKYLIEKIKLHDMQEGKCLYS LEAIPLEDLLNNPFNYEVDHIIPRSVSFDNSFNNKVLVKQEENSKKGNRTPFQ YLSSSDSKISYETFKKHILNLAKGKGRISKTKKEYLLEERDINRFSVQKDFINRNL VDTRYATRGLMNLLRSYFRVNNLDVKVKSINGGFTSFLRRKWKFKKERNKG YKHHAEDALIIANADFIFKEWKKLDKAKKVMENQMFEEKQAESMPEIETEQ EYKEIFITPHQIKHIKDFKDYKYSHRVDKKPNRELINDTLYSTRKDDKGNTLIVN NLNGLYDKDNDKLKKLINKSPEKLLMYHHDPQTYQKLKLIMEQYGDEKNPL YKYYEETGNYLTKYSKKDNGPVIKKIKYYGNKLNAHLDITDDYPNSRNKVVKL SLKPYRFDVYLDNGVYKFVTVKNLDVIKKENYYEVNSKCYEEAKKLKKISNQA EFIASFYNNDLIKINGELYRVIGVNNDLLNRIEVNMIDITYREYLENMNDKRPP RIIKTIASKTQSIKKYSTDILGNLYEVKSKKHPQIIKKG SauCas9-KKH Staphylococcus aureus MKRNYILGLDIGITSVGYGIIDYETRDVIDAGVRLFKEANVENNEGRRSKRGA 9,004 N580A H557A D10A RRLKRRRRHRIQRVKKLLFDYNLLTDHSELSGINPYEARVKGLSQKLSEEEFSA ALLHLAKRRGVHNVNEVEEDTGNELSTKEQISRNSKALEEKYVAELQLERLKK DGEVRGSINRFKTSDYVKEAKQLLKVQKAYHQLDQSFIDTYIDLLETRRTYYE GPGEGSPFGWKDIKEWYEMLMGHCTYFPEELRSVKYAYNADLYNALNDLN NLVITRDENEKLEYYEKFQIIENVFKQKKKPTLKQIAKEILVNEEDIKGYRVTST GKPEFTNLKVYHDIKDITARKEIIENAELLDQIAKILTIYQSSEDIQEELTNLNSE LTQEEIEQISNLKGYTGTHNLSLKAINLILDELWHTNDNQIAIFNRLKLVPKKV DLSQQKEIPTTLVDDFILSPVVKRSFIQSIKVINAIIKKYGLPNDIIIELAREKNSK DAQKMINEMQKRNRQTNERIEEIIRTTGKENAKYLIEKIKLHDMQEGKCLYS LEAIPLEDLLNNPFNYEVDHIIPRSVSFDNSFNNKVLVKQEENSKKGNRTPFQ YLSSSDSKISYETFKKHILNLAKGKGRISKTKKEYLLEERDINRFSVQKDFINRNL VDTRYATRGLMNLLRSYFRVNNLDVKVKSINGGFTSFLRRKWKFKKERNKG YKHHAEDALIIANADFIFKEWKKLDKAKKVMENQMFEEKQAESMPEIETEQ EYKEIFITPHQIKHIKDFKDYKYSHRVDKKPNRKLINDTLYSTRKDDKGNTLIV NNLNGLYDKDNDKLKKLINKSPEKLLMYHHDPQTYQKLKLIMEQYGDEKNP LYKYYEETGNYLTKYSKKDNGPVIKKIKYYGNKLNAHLDITDDYPNSRNKVVK LSLKPYRFDVYLDNGVYKFVTVKNLDVIKKENYYEVNSKCYEEAKKLKKISNQ AEFIASFYKNDLIKINGELYRVIGVNNDLLNRIEVNMIDITYREYLENMNDKRP PHIIKTIASKTQSIKKYSTDILGNLYEVKSKKHPQIIKKG SauriCas9 Staphylococcus auricularis MQENQQKQNYILGLDIGITSVGYGLIDSKTREVIDAGVRLFPEADSENNSNR 9.005 N588A H565A D15A RSKRGARRLKRRRIHRLNRVKDLLADYQMIDLNNVPKSTDPYTIRVKGLREPL TKEEFAIALLHIAKRRGLHNISVSMGDEEQDNELSTKQQLQKNAQQLQDKY VCELQLERLTNINKVRGEKNRFKTEDFVKEVKQLCETQRQYHNIDDQFIQQY IDLVSTRREYFEGPGNGSPYGWDGDLLKWYEKLMGRCTYFPEELRSVKYAYS ADLFNALNDLNNLVVTRDDNPKLEYYEKYHIIENVFKQKKNPTLKQIAKEIGV QDYDIRGYRITKSGKPQFTSFKLYHDLKNIFEQAKYLEDVEMLDEIAKILTIYQ DEISIKKALDQLPELLTESEKSQIAQLTGYTGTHRLSLKCIHIVIDELWESPENQ MEIFTRLNLKPKKVEMSEIDSIPTTLVDEFILSPVVKRAFIQSIKVINAVINRFGL PEDIIIELAREKNSKDRRKFINKLQKQNEATRKKIEQLLAKYGNTNAKYMIEKI KLHDMQEGKCLYSLEAIPLEDLLSNPTHYEVDHIIPRSVSFDNSLNNKVLVKQ SENSKKGNRTPYQYLSSNESKISYNQFKQHILNLSKAKDRISKKKRDMLLEER DINKFEVQKEFINRNLVDTRYATRELSNLLKTYFSTHDYAVKVKTINGGFTNH LRKVWDFKKHRNHGYKHHAEDALVIANADFLFKTHKALRRTDKILEQPGLE VNDTTVKVDTEEKYQELFETPKQVKNIKQFRDFKYSHRVDKKPNRQLINDTL YSTREIDGETYVVQTLKDLYAKDNEKVKKLFTERPQKILMYQHDPKTFEKLM TILNQYAEAKNPLAAYYEDKGEYVTKYAKKGNGPAIHKIKYIDKKLGSYLDVS NKYPETQNKLVKLSLKSFRFDIYKCEQGYKMVSIGYLDVLKKDNYYYIPKDKYE AEKQKKKIKESDLFVGSFYYNDLIMYEDELFRVIGVNSDINNLVELNMVDITY KDFCEVNNVTGEKRIKKTIGKRVVLIEKYTTDILGNLYKTPLPKKPQLIFKRGEL SaruCas9-KKH Staphylococcus auricularis MQENQQKQNYILGLDIGITSVGYGLIDSKTREVIDAGVRLFPEADSENNSNR 9,006 N588A H565A D15A RSKRGARRLKRRRIHRLNRVKDLLADYQMIDLNNVPKSTDPYTIRVKGLREPL TKEEFAIALLHIAKRRGLHNISVSMGDEEQDNELSTKQQLQKNAQQLQDKY VCELQLERLTNINKVRGEKNRFKTEDFVKEVKQLCETQRQYHNIDDQFIQQY IDLVSTRREYFEGPGNGSPYGWDGDLLKWYEKLMGRCTYFPEELRSVKYAYS ADLFNALNDLNNLVVTRDDNPKLEYYEKYHIIENVFKQKKNPTLKQIAKEIGV QDYDIRGYRITKSGKPQFTSFKLYHDLKNIFEQAKYLEDVEMLDEIAKILTIYQ DEISIKKALDQLPELLTESEKSQIAQLTGYTGTHRLSLKCIHIVIDELWESPENQ MEIFTRLNLKPKKVEMSEIDSIPTTLVDEFILSPVVKRAFIQSIKVINAVINRFGL PEDIIIELAREKNSKDRRKFINKLQKQNEATRKKIEQLLAKYGNTNAKYMIEKI KLHDMQEGKCLYSLEAIPLEDLLSNPTHYEVDHIIPRSVSFDNSLNNKVLVKQ SENSKKGNRTPYQYLSSNESKISYNQFKQHILNLSKAKDRISKKKRDMLLEER DINKFEVQKEFINRNLVDTRYATRELSNLLKTYFSTHDYAVKVKTINGGFTNH LRKVWDFKKHRNHGYKHHAEDALVIANADFLFKTHKALRRTDKILEQPGLE VNDTTVKVDTEEKYQELFETPKQVKNIKQFRDFKYSHRVDKKPNRKLINDTL YSTREIDGETYVVQTLKDLYAKDNEKVKKLFTERPQKILMYQHDPKTFEKLM TILNQYAEAKNPLAAYYEDKGEYVTKYAKKGNGPAIHKIKYIDKKLGSYLDVS NKYPETQNKLVKLSLKSFRFDIYKCEQGYKMVSIGYLDVLKKDNYYYIPKDKYE AEKQKKKIKESDLFVGSFYKNDLIMYEDELFRVIGVNSDINNLVELNMVDITY KDFCEVNNVTGEKHIKKTIGKRVVLIEKYTTDILGNLYKTPLPKKPQLIFKRGEL ScaCas9-Sc++ Streptococcus canis MEKKYSIGLDIGTNSVGWAVITDDYKVPSKKFKVLGNTNRKSIKKNLMGALL 9,007 N872A H849A D10A FDSGETAEATRLKRTARRRYTRRKNRIRYLQEIFANEMAKLDDSFFQRLEESF LVEEDKKNERHPIFGNLADEVAYHRNYPTIYHLRKKLADSPEKADLRLIYLALA HIIKFRGHFLIEGKLNAENSDVAKLFYQLIQTYNQLFEESPLDEIEVDAKGILSA RLSKSKRLEKLIAVFPNEKKNGLFGNIIALALGLTPNFKSNFDLTEDAKLQLSKD TYDDDLDELLGQIGDQYADLFSAAKNLSDAILLSDILRSNSEVTKAPLSASMV KRYDEHHQDLALLKTLVRQQFPEKYAEIFKDDTKNGYAGYVGADKKLRKRS GKLATEEEFYKFIKPILEKMDGAEELLAKLNRDDLLRKQRTFDNGSIPHQIHLK ELHAILRRQEEFYPFLKENREKIEKILTFRIPYYVGPLARGNSRFAWLTRKSEEA ITPWNFEEVVDKGASAQSFIERMTNFDEQLPNKKVLPKHSLLYEYFTVYNEL TKVKYVTERMRKPEFLSGEQKKAIVDLLFKTNRKVTVKQLKEDYFKKIECFDS VEIIGVEDRFNASLGTYHDLLKIIKDKDFLDNEENEDILEDIVLTLTLFEDREMIE ERLKTYAHLFDDKVMKQLKRRHYTGWGRLSRKMINGIRDKQSGKTILDFLKS DGFSNRNFMQLIHDDSLTFKEEIEKAQVSGQGDSLHEQIADLAGSPAIKKGIL QTVKIVDELVKVMGHKPENIVIEMARENQTTTKGLQQSRERKKRIEEGIKELE SQILKENPVENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDYDVDHIVP QSFIKDDSIDNKVLTRSVENRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQ RKFDNLTKAERGGLSEADKAGFIKRQLVETRQITKHVARILDSRMNTKRDKN DKPIREVKVITLKSKLVSDFRKDFQLYKVRDINNYHHAHDAYLNAVVGTALIK KYPKLESEFVYGDYKVYDVRKMIAKSEQEIGKATAKRFFYSNIMNFFKTEVKL ANGEIRKRPLIETNGETGEVVWNKEKDFATVRKVLAMPQVNIVKKTEVQTG GFSKESILSKRESAKLIPRKKGWDTRKYGGFGSPTVAYSILVVAKVEKGKAKKL KSVKVLVGITIMEKGSYEKDPIGFLEAKGYKDIKKELIFKLPKYSLFELENGRRR MLASAKELQKANELVLPQHLVRLLYYTQNISATTGSNNLGYIEQHREEFKEIF EKIIDFSEKYILKNKVNSNLKSSFDEQFAVSDSILLSNSFVSLLKYTSFGASGGFT FLDLDVKQGRLRYQTVTEVLDATLIYQSITGLYETRTDLSQLGGD SpyCas9 Streptococcus pyogenes MDKKYSIGLDIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLF 9,008 N863A H840A D10A DSGETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFL VEEDKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLALAH MIKFRGHFLIEGDLNPDNSDVDKLFIQLVQTYNQLFEENPINASGVDAKAILS ARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGLTPNFKSNFDLAEDAKLQLS KDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILLSDILRVNTEITKAPLSAS MIKRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSKNGYAGYIDGGASQEEF YKFIKPILEKMDGTEELLVKLNREDLLRKQRTFDNGSIPHQIHLGELHAILRRQ EDFYPFLKDNREKIEKILTFRIPYYVGPLARGNSRFAWMTRKSEETITPWNFE EVVDKGASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYFTVYNELTKVKYVTE GMRKPAFLSGEQKKAIVDLLFKTNRKVTVKQLKEDYFKKIECFDSVEISGVED RFNASLGTYHDLLKIIKDKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYA HLFDDKVMKQLKRRRYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANR NFMQLIHDDSLTFKEDIQKAQVSGQGDSLHEHIANLAGSPAIKKGILQTVKV VDELVKVMGRHKPENIVIEMARENQTTQKGQKNSRERMKRIEEGIKELGSQ ILKEHPVENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDYDVDHIVPQSF LKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQRKF DNLTKAERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLI REVKVITLKSKLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPK LESEFVYGDYKVYDVRKMIAKSEQEIGKATAKYFFYSNIMNFFKTEITLANGEI RKRPLIETNGETGEIVWDKGRDFATVRKVLSMPQVNIVKKTEVQTGGFSKES ILPKRNSDKLIARKKDWDPKKYGGFDSPTVAYSVLVVAKVEKGKSKKLKSVKE LLGITIMERSSFEKNPIDFLEAKGYKEVKKDLIIKLPKYSLFELENGRKRMLASA GELQKGNELALPSKYVNFLYLASHYEKLKGSPEDNEQKQLFVEQHKHYLDEII EQISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENIIHLFTLTNLGAPAAF KYFDTTIDRKRYTSTKEVLDATLIHQSITGLYETRIDLSQLGGD SpyCas9-NG Streptococcus pyogenes MDKKYSIGLDIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLF 9,009 N863A H840A D10A DSGETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFL VEEDKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLALAH MIKFRGHFLIEGDLNPDNSDVDKLFIQLVQTYNQLFEENPINASGVDAKAILS ARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGLTPNFKSNFDLAEDAKLQLS KDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILLSDILRVNTEITKAPLSAS MIKRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSKNGYAGYIDGGASQEEF YKFIKPILEKMDGTEELLVKLNREDLLRKQRTFDNGSIPHQIHLGELHAILRRQ EDFYPFLKDNREKIEKILTFRIPYYVGPLARGNSRFAWMTRKSEETITPWNFE EVVDKGASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYFTVYNELTKVKYVTE GMRKPAFLSGEQKKAIVDLLFKTNRKVTVKQLKEDYFKKIECFDSVEISGVED RFNASLGTYHDLLKIIKDKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYA HLFDDKVMKQLKRRRYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANR NFMQLIHDDSLTFKEDIQKAQVSGQGDSLHEHIANLAGSPAIKKGILQTVKV VDELVKVMGRHKPENIVIEMARENQTTQKGQKNSRERMKRIEEGIKELGSQ ILKEHPVENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDYDVDHIVPQSF LKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQRKF DNLTKAERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLI REVKVITLKSKLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPK LESEFVYGDYKVYDVRKMIAKSEQEIGKATAKYFFYSNIMNFFKTEITLANGEI RKRPLIETNGETGEIVWDKGRDFATVRKVLSMPQVNIVKKTEVQTGGFSKES IRPKRNSDKLIARKKDWDPKKYGGFVSPTVAYSVLVVAKVEKGKSKKLKSVKE LLGITIMERSSFEKNPIDFLEAKGYKEVKKDLIIKLPKYSLFELENGRKRMLASA RFLQKGNELALPSKYVNFLYLASHYEKLKGSPEDNEQKQLFVEQHKHYLDEII EQISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENIIHLFTLTNLGAPRAF KYFDTTIDRKVYRSTKEVLDATLIHQSITGLYETRIDLSQLGGD SpyCas9-SpRY Streptococcus pyogenes MDKKYSIGLDIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLF 9,010 N863A H840A D10A DSGETAERTRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFL VEEDKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLALAH MIKFRGHFLIEGDLNPDNSDVDKLFIQLVQTYNQLFEENPINASGVDAKAILS ARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGLTPNFKSNFDLAEDAKLQLS KDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILLSDILRVNTEITKAPLSAS MIKRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSKNGYAGYIDGGASQEEF YKFIKPILEKMDGTEELLVKLNREDLLRKQRTFDNGSIPHQIHLGELHAILRRQ EDFYPFLKDNREKIEKILTFRIPYYVGPLARGNSRFAWMTRKSEETITPWNFE EVVDKGASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYFTVYNELTKVKYVTE GMRKPAFLSGEQKKAIVDLLFKTNRKVTVKQLKEDYFKKIECFDSVEISGVED RFNASLGTYHDLLKIIKDKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYA HLFDDKVMKQLKRRRYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANR NFMQLIHDDSLTFKEDIQKAQVSGQGDSLHEHIANLAGSPAIKKGILQTVKV VDELVKVMGRHKPENIVIEMARENQTTQKGQKNSRERMKRIEEGIKELGSQ ILKEHPVENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDYDVDHIVPQSF LKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQRKF DNLTKAERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLI REVKVITLKSKLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPK LESEFVYGDYKVYDVRKMIAKSEQEIGKATAKYFFYSNIMNFFKTEITLANGEI RKRPLIETNGETGEIVWDKGRDFATVRKVLSMPQVNIVKKTEVQTGGFSKES IRPKRNSDKLIARKKDWDPKKYGGFLWPTVAYSVLVVAKVEKGKSKKLKSVK ELLGITIMERSSFEKNPIDFLEAKGYKEVKKDLIIKLPKYSLFELENGRKRMLAS AKQLQKGNELALPSKYVNFLYLASHYEKLKGSPEDNEQKQLFVEQHKHYLDE IIEQISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENIIHLFTLTRLGAPRAF KYFDTTIDPKQYRSTKEVLDATLIHQSITGLYETRIDLSQLGGD St1Cas9 Streptococcus thermophilus MSDLVLGLDIGIGSVGVGILNKVTGEIIHKNSRIFPAAQAENNLVRRTNRQG 9,011 N622A H599A D9A RRLARRKKHRRVRLNRLFEESGLITDFTKISINLNPYQLRVKGLTDELSNEELFI ALKNMVKHRGISYLDDASDDGNSSVGDYAQIVKENSKQLETKTPGQIQLER YQTYGQLRGDFTVEKDGKKHRLINVFPTSAYRSEALRILQTQQEFNPQITDEF INRYLEILTGKRKYYHGPGNEKSRTDYGRYRTSGETLDNIFGILIGKCTFYPDEF RAAKASYTAQEFNLLNDLNNLTVPTETKKLSKEQKNQIINYVKNEKAMGPAK LFKYIAKLLSCDVADIKGYRIDKSGKAEIHTFEAYRKMKTLETLDIEQMDRETL DKLAYVLTLNTEREGIQEALEHEFADGSFSQKQVDELVQFRKANSSIFGKGW HNFSVKLMMELIPELYETSEEQMTILTRLGKQKTTSSSNKTKYIDEKLLTEEIY NPVVAKSVRQAIKIVNAAIKEYGDFDNIVIEMARETNEDDEKKAIQKIQKAN KDEKDAAMLKAANQYNGKAELPHSVFHGHKQLATKIRLWHQQGERCLYT GKTISIHDLINNSNQFEVDHILPLSITFDDSLANKVLVYATANQEKGQRTPYQ ALDSMDDAWSFRELKAFVRESKTLSNKKKEYLLTEEDISKFDVRKKFIERNLV DTRYASRVVLNALQEHFRAHKIDTKVSVVRGQFTSQLRRHWGIEKTRDTYH HHAVDALIIAASSQLNLWKKQKNTLVSYSEDQLLDIETGELISDDEYKESVFK APYQHFVDTLKSKEFEDSILFSYQVDSKFNRKISDATIYATRQAKVGKDKADE TYVLGKIKDIYTQDGYDAFMKIYKKDKSKFLMYRHDPQTFEKVIEPILENYPN KQINEKGKEVPCNPFLKYKEEHGYIRKYSKKGNGPEIKSLKYYDSKLGNHIDIT PKDSNNKVVLQSVSPWRADVYFNKTTGKYEILGLKYADLQFEKGTGTYKISQ EKYNDIKKKEGVDSDSEFKFTLYKNDLLLVKDTETKEQQLFRFLSRTMPKQKH YVELKPYDKQKFEGGEALIKVLGNVANSGQCKKGLGKSNISIYKVRTDVLGN QHIIKNEGDKPKLDF BlatCas9 Brevibacillus laterosporus MAYTMGIDVGIASCGWAIVDLERQRIIDIGVRTFEKAENPKNGEALAVPRRE 9,012 N607A H584A D8A ARSSRRRLRRKKHRIERLKHMFVRNGLAVDIQHLEQTLRSQNEIDVWQLRV DGLDRMLTQKEWLRVLIHLAQRRGFQSNRKTDGSSEDGQVLVNVTENDRL MEEKDYRTVAEMMVKDEKFSDHKRNKNGNYHGVVSRSSLLVEIHTLFETQ RQHHNSLASKDFELEYVNIWSAQRPVATKDQIEKMIGTCTFLPKEKRAPKAS WHFQYFMLLQTINHIRITNVQGTRSLNKEEIEQVVNMALTKSKVSYHDTRKI LDLSEEYQFVGLDYGKEDEKKKVESKETIIKLDDYHKLNKIFNEVELAKGETWE ADDYDTVAYALTFFKDDEDIRDYLQNKYKDSKNRLVKNLANKEYTNELIGKV STLSFRKVGHLSLKALRKIIPFLEQGMTYDKACQAAGFDFQGISKKKRSVVLP VIDQISNPVVNRALTQTRKVINALIKKYGSPETIHIETARELSKTFDERKNITKD YKENRDKNEHAKKHLSELGIINPTGLDIVKYKLWCEQQGRCMYSNQPISFER LKESGYTEVDHIIPYSRSMNDSYNNRVLVMTRENREKGNQTPFEYMGNDT QRWYEFEQRVTTNPQIKKEKRQNLLLKGFTNRRELEMLERNLNDTRYITKYL SHFISTNLEFSPSDKKKKVVNTSGRITSHLRSRWGLEKNRGQNDLHHAMDAI VIAVTSDSFIQQVTNYYKRKERRELNGDDKFPLPWKFFREEVIARLSPNPKEQ IEALPNHFYSEDELADLQPIFVSRMPKRSITGEAHQAQFRRVVGKTKEGKNIT AKKTALVDISYDKNGDFNMYGRETDPATYEAIKERYLEFGGNVKKAFSTDLH KPKKDGTKGPLIKSVRIMENKTLVHPVNKGKGVVYNSSIVRTDVFQRKEKYY LLPVYVTDVTKGKLPNKVIVAKKGYHDWIEVDDSFTFLFSLYPNDLIFIRQNPK KKISLKKRIESHSISDSKEVQEIHAYYKGVDSSTAAIEFIIHDGSYYAKGVGVQN LDCFEKYQVDILGNYFKVKGEKRLELETSDSNHKGKDVNSIKSTSR cCas9-v16 Staphylococcus aureus MKRNYILGLDIGITSVGYGIIDYETRDVIDAGVRLFKEANVENNEGRRSKRGA 9,013 N580A  H557A D10A RRLKRRRRHRIQRVKKLLFDYNLLTDHSELSGINPYEARVKGLSQKLSEEEFSA ALLHLAKRRGVHNVNEVEEDTGNELSTKEQISRNSKALEEKYVAELQLERLKK DGEVRGSINRFKTSDYVKEAKQLLKVQKAYHQLDQSFIDTYIDLLETRRTYYE GPGEGSPFGWKDIKEWYEMLMGHCTYFPEELRSVKYAYNADLYNALNDLN NLVITRDENEKLEYYEKFQIIENVFKQKKKPTLKQIAKEILVNEEDIKGYRVTST GKPEFTNLKVYHDIKDITARKEIIENAELLDQIAKILTIYQSSEDIQEELTNLNSE LTQEEIEQISNLKGYTGTHNLSLKAINLILDELWHTNDNQIAIFNRLKLVPKKV DLSQQKEIPTTLVDDFILSPVVKRSFIQSIKVINAIIKKYGLPNDIIIELAREKNSK DAQKMINEMQKRNRQTNERIEEIIRTTGKENAKYLIEKIKLHDMQEGKCLYS LEAIPLEDLLNNPFNYEVDHIIPRSVSFDNSFNNKVLVKQEENSKKGNRTPFQ YLSSSDSKISYETFKKHILNLAKGKGRISKTKKEYLLEERDINRFSVQKDFINRNL VDTRYATRGLMNLLRSYFRVNNLDVKVKSINGGFTSFLRRKWKFKKERNKG YKHHAEDALIIANADFIFKEWKKLDKAKKVMENQMFEEKQAESMPEIETEQ EYKEIFITPHQIKHIKDFKDYKYSHRVDKKPNRKLINDTLYSTRKDDKGNTLIV NNLNGLYDKDNDKLKKLINKSPEKLLMYHHDPQTYQKLKLIMEQYGDEKNP LYKYYEETGNYLTKYSKKDNGPVIKKIKYYGNKLNAHLDITDDYPNSRNKVVK LSLKPYRFDVYLDNGVYKFVTVKNLDVIKKENYYEVNSKCYEEAKKLKKISNQ AEFIASFYKNDLIKINGELYRVIGVNSDKNNLIEVNMIDITYREYLENMNDKRP PHIIKTIASKTQSIKKYSTDILGNLYEVKSKKHPQIIKKG cCas9-v17 Staphylococcus aureus MKRNYILGLDIGITSVGYGIIDYETRDVIDAGVRLFKEANVENNEGRRSKRGA 9,014 N580A H557A D10A RRLKRRRRHRIQRVKKLLFDYNLLTDHSELSGINPYEARVKGLSQKLSEEEFSA ALLHLAKRRGVHNVNEVEEDTGNELSTKEQISRNSKALEEKYVAELQLERLKK DGEVRGSINRFKTSDYVKEAKQLLKVQKAYHQLDQSFIDTYIDLLETRRTYYE GPGEGSPFGWKDIKEWYEMLMGHCTYFPEELRSVKYAYNADLYNALNDLN NLVITRDENEKLEYYEKFQIIENVFKQKKKPTLKQIAKEILVNEEDIKGYRVTST GKPEFTNLKVYHDIKDITARKEIIENAELLDQIAKILTIYQSSEDIQEELTNLNSE LTQEEIEQISNLKGYTGTHNLSLKAINLILDELWHTNDNQIAIFNRLKLVPKKV DLSQQKEIPTTLVDDFILSPVVKRSFIQSIKVINAIIKKYGLPNDIIIELAREKNSK DAQKMINEMQKRNRQTNERIEEIIRTTGKENAKYLIEKIKLHDMQEGKCLYS LEAIPLEDLLNNPFNYEVDHIIPRSVSFDNSFNNKVLVKQEENSKKGNRTPFQ YLSSSDSKISYETFKKHILNLAKGKGRISKTKKEYLLEERDINRFSVQKDFINRNL VDTRYATRGLMNLLRSYFRVNNLDVKVKSINGGFTSFLRRKWKFKKERNKG YKHHAEDALIIANADFIFKEWKKLDKAKKVMENQMFEEKQAESMPEIETEQ EYKEIFITPHQIKHIKDFKDYKYSHRVDKKPNRKLINDTLYSTRKDDKGNTLIV NNLNGLYDKDNDKLKKLINKSPEKLLMYHHDPQTYQKLKLIMEQYGDEKNP LYKYYEETGNYLTKYSKKDNGPVIKKIKYYGNKLNAHLDITDDYPNSRNKVVK LSLKPYRFDVYLDNGVYKFVTVKNLDVIKKENYYEVNSKCYEEAKKLKKISNQ AEFIASFYKNDLIKINGELYRVIGVNNSTRNIVELNMIDITYREYLENMNDKRP PHIIKTIASKTQSIKKYSTDILGNLYEVKSKKHPQIIKKG cCas9-v21 Staphylococcus aureus MKRNYILGLDIGITSVGYGIIDYETRDVIDAGVRLFKEANVENNEGRRSKRGA 9,015 N580A H557A D10A RRLKRRRRHRIQRVKKLLFDYNLLTDHSELSGINPYEARVKGLSQKLSEEEFSA ALLHLAKRRGVHNVNEVEEDTGNELSTKEQISRNSKALEEKYVAELQLERLKK DGEVRGSINRFKTSDYVKEAKQLLKVQKAYHQLDQSFIDTYIDLLETRRTYYE GPGEGSPFGWKDIKEWYEMLMGHCTYFPEELRSVKYAYNADLYNALNDLN NLVITRDENEKLEYYEKFQIIENVFKQKKKPTLKQIAKEILVNEEDIKGYRVTST GKPEFTNLKVYHDIKDITARKEIIENAELLDQIAKILTIYQSSEDIQEELTNLNSE LTQEEIEQISNLKGYTGTHNLSLKAINLILDELWHTNDNQIAIFNRLKLVPKKV DLSQQKEIPTTLVDDFILSPVVKRSFIQSIKVINAIIKKYGLPNDIIIELAREKNSK DAQKMINEMQKRNRQTNERIEEIIRTTGKENAKYLIEKIKLHDMQEGKCLYS LEAIPLEDLLNNPFNYEVDHIIPRSVSFDNSFNNKVLVKQEENSKKGNRTPFQ YLSSSDSKISYETFKKHILNLAKGKGRISKTKKEYLLEERDINRFSVQKDFINRNL VDTRYATRGLMNLLRSYFRVNNLDVKVKSINGGFTSFLRRKWKFKKERNKG YKHHAEDALIIANADFIFKEWKKLDKAKKVMENQMFEEKQAESMPEIETEQ EYKEIFITPHQIKHIKDFKDYKYSHRVDKKPNRKLINDTLYSTRKDDKGNTLIV NNLNGLYDKDNDKLKKLINKSPEKLLMYHHDPQTYQKLKLIMEQYGDEKNP LYKYYEETGNYLTKYSKKDNGPVIKKIKYYGNKLNAHLDITDDYPNSRNKVVK LSLKPYRFDVYLDNGVYKFVTVKNLDVIKKENYYEVNSKCYEEAKKLKKISNQ AEFIASFYKNDLIKINGELYRVIGVNSDDRNIIELNMIDITYREYLENMNDKRP PHIIKTIASKTQSIKKYSTDILGNLYEVKSKKHPQIIKKG cCas9-v42 Staphylococcus aureus MKRNYILGLDIGITSVGYGIIDYETRDVIDAGVRLFKEANVENNEGRRSKRGA 9,016 N580A H557A D10A RRLKRRRRHRIQRVKKLLFDYNLLTDHSELSGINPYEARVKGLSQKLSEEEFSA ALLHLAKRRGVHNVNEVEEDTGNELSTKEQISRNSKALEEKYVAELQLERLKK DGEVRGSINRFKTSDYVKEAKQLLKVQKAYHQLDQSFIDTYIDLLETRRTYYE GPGEGSPFGWKDIKEWYEMLMGHCTYFPEELRSVKYAYNADLYNALNDLN NLVITRDENEKLEYYEKFQIIENVFKQKKKPTLKQIAKEILVNEEDIKGYRVTST GKPEFTNLKVYHDIKDITARKEIIENAELLDQIAKILTIYQSSEDIQEELTNLNSE LTQEEIEQISNLKGYTGTHNLSLKAINLILDELWHTNDNQIAIFNRLKLVPKKV DLSQQKEIPTTLVDDFILSPVVKRSFIQSIKVINAIIKKYGLPNDIIIELAREKNSK DAQKMINEMQKRNRQTNERIEEIIRTTGKENAKYLIEKIKLHDMQEGKCLYS LEAIPLEDLLNNPFNYEVDHIIPRSVSFDNSFNNKVLVKQEENSKKGNRTPFQ YLSSSDSKISYETFKKHILNLAKGKGRISKTKKEYLLEERDINRFSVQKDFINRNL VDTRYATRGLMNLLRSYFRVNNLDVKVKSINGGFTSFLRRKWKFKKERNKG YKHHAEDALIIANADFIFKEWKKLDKAKKVMENQMFEEKQAESMPEIETEQ EYKEIFITPHQIKHIKDFKDYKYSHRVDKKPNRKLINDTLYSTRKDDKGNTLIV NNLNGLYDKDNDKLKKLINKSPEKLLMYHHDPQTYQKLKLIMEQYGDEKNP LYKYYEETGNYLTKYSKKDNGPVIKKIKYYGNKLNAHLDITDDYPNSRNKVVK LSLKPYRFDVYLDNGVYKFVTVKNLDVIKKENYYEVNSKCYEEAKKLKKISNQ AEFIASFYKNDLIKINGELYRVIGVNNNRLNKIELNMIDITYREYLENMNDKRP PHIIKTIASKTQSIKKYSTDILGNLYEVKSKKHPQIIKKG CdiCas9 Corynebacterium diphtheriae MKYHVGIDVGTFSVGLAAIEVDDAGMPIKTLSLVSHIHDSGLDPDEIKSAVT 9,017 N597A H573A D8A RLASSGIARRTRRLYRRKRRRLQQLDKFIQRQGWPVIELEDYSDPLYPWKVR AELAASYIADEKERGEKLSVALRHIARHRGWRNPYAKVSSLYLPDGPSDAFK AIREEIKRASGQPVPETATVGQMVTLCELGTLKLRGEGGVLSARLQQSDYAR EIQEICRMQEIGQELYRKIIDVVFAAESPKGSASSRVGKDPLQPGKNRALKAS DAFQRYRIAALIGNLRVRVDGEKRILSVEEKNLVFDHLVNLTPKKEPEWVTIA EILGIDRGQLIGTATMTDDGERAGARPPTHDTNRSIVNSRIAPLVDWWKTA SALEQHAMVKALSNAEVDDFDSPEGAKVQAFFADLDDDVHAKLDSLHLPV GRAAYSEDTLVRLTRRMLSDGVDLYTARLQEFGIEPSWTPPTPRIGEPVGNP AVDRVLKTVSRWLESATKTWGAPERVIIEHVREGFVTEKRAREMDGDMRR RAARNAKLFQEMQEKLNVQGKPSRADLWRYQSVQRQNCQCAYCGSPITF SNSEMDHIVPRAGQGSTNTRENLVAVCHRCNQSKGNTPFAIWAKNTSIEG VSVKEAVERTRHWVTDTGMRSTDFKKFTKAVVERFQRATMDEEIDARSME SVAWMANELRSRVAQHFASHGTTVRVYRGSLTAEARRASGISGKLKFFDGV GKSRLDRRHHAIDAAVIAFTSDYVAETLAVRSNLKQSQAHRQEAPQWREFT GKDAEHRAAWRVWCQKMEKLSALLTEDLRDDRVVVMSNVRLRLGNGSA HKETIGKLSKVKLSSQLSVSDIDKASSEALWCALTREPGFDPKEGLPANPERHI RVNGTHVYAGDNIGLFPVSAGSIALRGGYAELGSSFHHARVYKITSGKKPAF AMLRVYTIDLLPYRNQDLFSVELKPQTMSMRQAEKKLRDALATGNAEYLG WLVVDDELVVDTSKIATDQVKAVEAELGTIRRWRVDGFFSPSKLRLRPLQM SKEGIKKESAPELSKIIDRPGWLPAVNKLFSDGNVTVVRRDSLGRVRLESTAH LPVTWKVQ CjeCas9 Campylobacter jejuni MARILAFDIGISSIGWAFSENDELKDCGVRIFTKVENPKTGESLALPRRLARSA 9,018 N582A H559A D8A RKRLARRKARLNHLKHLIANEFKLNYEDYQSFDESLAKAYKGSLISPYELRFRA LNELLSKQDFARVILHIAKRRGYDDIKNSDDKEKGAILKAIKQNEEKLANYQS VGEYLYKEYFQKFKENSKEFTNVRNKKESYERCIAQSFLKDELKLIFKKQREFG FSFSKKFEEEVLSVAFYKRALKDFSHLVGNCSFFTDEKRAPKNSPLAFMFVAL TRIINLLNNLKNTEGILYTKDDLNALLNEVLKNGTLTYKQTKKLLGLSDDYEFK GEKGTYFIEFKKYKEFIKALGEHNLSQDDLNEIAKDITLIKDEIKLKKALAKYDLN QNQIDSLSKLEFKDHLNISFKALKLVTPLMLEGKKYDEACNELNLKVAINEDK KDFLPAFNETYYKDEVTNPVVLRAIKEYRKVLNALLKKYGKVHKINIELAREVG KNHSQRAKIEKEQNENYKAKKDAELECEKLGLKINSKNILKLRLFKEQKEFCAY SGEKIKISDLQDEKMLEIDHIYPYSRSFDDSYMNKVLVFTKQNQEKLNQTPFE AFGNDSAKWQKIEVLAKNLPTKKQKRILDKNYKDKEQKNFKDRNLNDTRYI ARLVLNYTKDYLDFLPLSDDENTKLNDTQKGSKVHVEAKSGMLTSALRHTW GFSAKDRNNHLHHAIDAVIIAYANNSIVKAFSDFKKEQESNSAELYAKKISELD YKNKRKFFEPFSGFRQKVLDKIDEIFVSKPERKKPSGALHEETFRKEEEFYQSY GGKEGVLKALELGKIRKVNGKIVKNGDMFRVDIFKHKKTNKFYAVPIYTMDF ALKVLPNKAVARSKKGEIKDWILMDENYEFCFSLYKDSLILIQTKDMQEPEFV YYNAFTSSTVSLIVSKHDNKFETLSKNQKILFKNANEKEVIAKSIGIQNLKVFEK YIVSALGEVTKAEFRQREDFKK GeoCas9 Geobacillus stearothermophilus MRYKIGLDIGITSVGWAVMNLDIPRIEDLGVRIFDRAENPQTGESLALPRRLA 9,019 N605A H582A D8A RSARRRLRRRKHRLERIRRLVIREGILTKEELDKLFEEKHEIDVWQLRVEALDR KLNNDELARVLLHLAKRRGFKSNRKSERSNKENSTMLKHIEENRAILSSYRTV GEMIVKDPKFALHKRNKGENYTNTIARDDLEREIRLIFSKQREFGNMSCTEEF ENEYITIWASQRPVASKDDIEKKVGFCTFEPKEKRAPKATYTFQSFIAWEHIN KLRLISPSGARGLTDEERRLLYEQAFQKNKITYHDIRTLLHLPDDTYFKGIVYDR GESRKQNENIRFLELDAYHQIRKAVDKVYGKGKSSSFLPIDFDTFGYALTLFKD DADIHSYLRNEYEQNGKRMPNLANKVYDNELIEELLNLSFTKFGHLSLKALRS ILPYMEQGEVYSSACERAGYTFTGPKKKQKTMLLPNIPPIANPVVMRALTQA RKVVNAIIKKYGSPVSIHIELARDLSQTFDERRKTKKEQDENRKKNETAIRQL MEYGLTLNPTGHDIVKFKLWSEQNGRCAYSLQPIEIERLLEPGYVEVDHVIPY SRSLDDSYTNKVLVLTRENREKGNRIPAEYLGVGTERWQQFETFVLTNKQFS KKKRDRLLRLHYDENEETEFKNRNLNDTRYISRFFANFIREHLKFAESDDKQK VYTVNGRVTAHLRSRWEFNKNREESDLHHAVDAVIVACTTPSDIAKVTAFY QRREQNKELAKKTEPHFPQPWPHFADELRARLSKHPKESIKALNLGNYDDQ KLESLQPVFVSRMPKRSVTGAAHQETLRRYVGIDERSGKIQTVVKTKLSEIKL DASGHFPMYGKESDPRTYEAIRQRLLEHNNDPKKAFQEPLYKPKKNGEPGP VIRTVKIIDTKNQVIPLNDGKTVAYNSNIVRVDVFEKDGKYYCVPVYTMDIM KGILPNKAIEPNKPYSEWKEMTEDYTFRFSLYPNDLIRIELPREKTVKTAAGEE INVKDVFVYYKTIDSANGGLELISHDHRFSLRGVGSRTLKRFEKYQVDVLGNI YKVRGEKRVGLASSAHSKPGKTIRPLQSTRD iSpyMacCas9 Streptococcus spp. MDKKYSIGLDIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLF 9,020 N863A H840A D10A DSGETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFL VEEDKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLALAH MIKFRGHFLIEGDLNPDNSDVDKLFIQLVQTYNQLFEENPINASGVDAKAILS ARLSKSRKLENLIAQLPGEKKNGLFGNLIALSLGLTPNFKSNFDLAEDAKLQLS KDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILLSDILRVNTEITKAPLSAS MIKRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSKNGYAGYIDGGASQEEF YKFIKPILEKMDGTEELLVKLKREDLLRKQRTFDNGSIPHQIHLGELHAILRRQ EDFYPFLKDNREKIEKILTFRIPYYVGPLARGNSRFAWMTRKSEETITPWNFE EVVDKGASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYFTVYNELTKVKYVTE GMRKPAFLSGEQKKAIVDLLFKTNRKVTVKQLKEDYFKKIECFDSVEISGVED RFNASLGTYHDLLKIIKDKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYA HLFDDKVMKQLKRRRYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANR NFMQLIHDDSLTFKEDIQKAQVSGQGDSLHEHIANLAGSPAIKKGILQTVKV VDELVKVMGRHKPENIVIEMARENQTTQKGQKNSRERMKRIEEGIKELGSQ ILKEHPVENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDYDVDHIVPQSF LKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQRKF DNLTKAERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLI REVKVITLKSKLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPK LESEFVYGDYKVYDVRKMIAKSEQEIGKATAKYFFYSNIMNFFKTEITLANGEI RKRPLIETNGETGEIVWDKGRDFATVRKVLSMPQVNIVKKTEIQTVGQNGG LFDDNPKSPLEVTPSKLVPLKKELNPKKYGGYQKPTTAYPVLLITDTKQLIPISV MNKKQFEQNPVKFLRDRGYQQVGKNDFIKLPKYTLVDIGDGIKRLWASSKEI HKGNQLVVSKKSQILLYHAHHLDSDLSNDYLQNHNQQFDVLFNEIISFSKKC KLGKEHIQKIENVYSNKKNSASIEELAESFIKLLGFTQLGATSPFNFLGVKLNQ KQYKGKKDYILPCTEGTLIRQSITGLYETRVDLSKIGEDSGGSGGSKRTADGSE FES NmeCas9 Neisseria meningitidis MAAFKPNSINYILGLDIGIASVGWAMVEIDEEENPIRLIDLGVRVFERAEVPK 9,021 N611A H588A D16A TGDSLAMARRLARSVRRLTRRRAHRLLRTRRLLKREGVLQAANFDENGLIKS LPNTPWQLRAAALDRKLTPLEWSAVLLHLIKHRGYLSQRKNEGETADKELG ALLKGVAGNAHALQTGDFRTPAELALNKFEKESGHIRNQRSDYSHTFSRKDL QAELILLFEKQKEFGNPHVSGGLKEGIETLLMTQRPALSGDAVQKMLGHCTF EPAEPKAAKNTYTAERFIWLTKLNNLRILEQGSERPLTDTERATLMDEPYRKS KLTYAQARKLLGLEDTAFFKGLRYGKDNAEASTLMEMKAYHAISRALEKEGL KDKKSPLNLSPELQDEIGTAFSLFKTDEDITGRLKDRIQPEILEALLKHISFDKFV QISLKALRRIVPLMEQGKRYDEACAEIYGDHYGKKNTEEKIYLPPIPADEIRNP VVLRALSQARKVINGVVRRYGSPARIHIETAREVGKSFKDRKEIEKRQEENRK DREKAAAKFREYFPNFVGEPKSKDILKLRLYEQQHGKCLYSGKEINLGRLNEK GYVEIDHALPFSRTWDDSFNNKVLVLGSENQNKGNQTPYEYFNGKDNSRE WQEFKARVETSRFPRSKKQRILLQKFDEDGFKERNLNDTRYVNRFLCQFVA DRMRLTGKGKKRVFASNGQITNLLRGFWGLRKVRAENDRHHALDAVVVA CSTVAMQQKITRFVRYKEMNAFDGKTIDKETGEVLHQKTHFPQPWEFFAQ EVMIRVFGKPDGKPEFEEADTLEKLRTLLAEKLSSRPEAVHEYVTPLFVSRAP NRKMSGQGHMETVKSAKRLDEGVSVLRVPLTQLKLKDLEKMVNREREPKL YEALKARLEAHKDDPAKAFAEPFYKYDKAGNRTQQVKAVRVEQVQKTGVW VRNHNGIADNATMVRVDVFEKGDKYYLVPIYSWQVAKGILPDRAVVQGKD EEDWQLIDDSFNFKFSLHPNDLVEVITKKARMFGYFASCHRGTGNINIRIHD LDHKIGKNGILEGIGVKTALSFQKYQIDELGKEIRPCRLKKRPPVR ScaCas9 Streptococcus canis MEKKYSIGLDIGTNSVGWAVITDDYKVPSKKFKVLGNTNRKSIKKNLMGALL 9,022 N872A H849A D10A FDSGETAEATRLKRTARRRYTRRKNRIRYLQEIFANEMAKLDDSFFQRLEESF LVEEDKKNERHPIFGNLADEVAYHRNYPTIYHLRKKLADSPEKADLRLIYLALA HIIKFRGHFLIEGKLNAENSDVAKLFYQLIQTYNQLFEESPLDEIEVDAKGILSA RLSKSKRLEKLIAVFPNEKKNGLFGNIIALALGLTPNFKSNFDLTEDAKLQLSKD TYDDDLDELLGQIGDQYADLFSAAKNLSDAILLSDILRSNSEVTKAPLSASMV KRYDEHHQDLALLKTLVRQQFPEKYAEIFKDDTKNGYAGYVGIGIKHRKRTT KLATQEEFYKFIKPILEKMDGAEELLAKLNRDDLLRKQRTFDNGSIPHQIHLKE LHAILRRQEEFYPFLKENREKIEKILTFRIPYYVGPLARGNSRFAWLTRKSEEAI TPWNFEEVVDKGASAQSFIERMTNFDEQLPNKKVLPKHSLLYEYFTVYNELT KVKYVTERMRKPEFLSGEQKKAIVDLLFKTNRKVTVKQLKEDYFKKIECFDSV EIIGVEDRFNASLGTYHDLLKIIKDKDFLDNEENEDILEDIVLTLTLFEDREMIEE RLKTYAHLFDDKVMKQLKRRHYTGWGRLSRKMINGIRDKQSGKTILDFLKS DGFSNRNFMQLIHDDSLTFKEEIEKAQVSGQGDSLHEQIADLAGSPAIKKGIL QTVKIVDELVKVMGHKPENIVIEMARENQTTTKGLQQSRERKKRIEEGIKELE SQILKENPVENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDYDVDHIVP QSFIKDDSIDNKVLTRSVENRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQ RKFDNLTKAERGGLSEADKAGFIKRQLVETRQITKHVARILDSRMNTKRDKN DKPIREVKVITLKSKLVSDFRKDFQLYKVRDINNYHHAHDAYLNAVVGTALIK KYPKLESEFVYGDYKVYDVRKMIAKSEQEIGKATAKRFFYSNIMNFFKTEVKL ANGEIRKRPLIETNGETGEVVWNKEKDFATVRKVLAMPQVNIVKKTEVQTG GFSKESILSKRESAKLIPRKKGWDTRKYGGFGSPTVAYSILVVAKVEKGKAKKL KSVKVLVGITIMEKGSYEKDPIGFLEAKGYKDIKKELIFKLPKYSLFELENGRRR MLASATELQKANELVLPQHLVRLLYYTQNISATTGSNNLGYIEQHREEFKEIF EKIIDFSEKYILKNKVNSNLKSSFDEQFAVSDSILLSNSFVSLLKYTSFGASGGFT FLDLDVKQGRLRYQTVTEVLDATLIYQSITGLYETRTDLSQLGGD ScaCas9-HiFi-Sc++ Streptococcus canis MEKKYSIGLDIGTNSVGWAVITDDYKVPSKKFKVLGNTNRKSIKKNLMGALL 9,023 N872A H849A D10A FDSGETAEATRLKRTARRRYTRRKNRIRYLQEIFANEMAKLDDSFFQRLEESF LVEEDKKNERHPIFGNLADEVAYHRNYPTIYHLRKKLADSPEKADLRLIYLALA HIIKFRGHFLIEGKLNAENSDVAKLFYQLIQTYNQLFEESPLDEIEVDAKGILSA RLSKSKRLEKLIAVFPNEKKNGLFGNIIALALGLTPNFKSNFDLTEDAKLQLSKD TYDDDLDELLGQIGDQYADLFSAAKNLSDAILLSDILRSNSEVTKAPLSASMV KRYDEHHQDLALLKTLVRQQFPEKYAEIFKDDTKNGYAGYVGADKKLRKRS GKLATEEEFYKFIKPILEKMDGAEELLAKLNRDDLLRKQRTFDNGSIPHQIHLK ELHAILRRQEEFYPFLKENREKIEKILTFRIPYYVGPLARGNSRFAWLTRKSEEA ITPWNFEEVVDKGASAQSFIERMTNFDEQLPNKKVLPKHSLLYEYFTVYNEL TKVKYVTERMRKPEFLSGEQKKAIVDLLFKTNRKVTVKQLKEDYFKKIECFDS VEIIGVEDRFNASLGTYHDLLKIIKDKDFLDNEENEDILEDIVLTLTLFEDREMIE ERLKTYAHLFDDKVMKQLKRRHYTGWGRLSRKMINGIRDKQSGKTILDFLKS DGFSNANFMQLIHDDSLTFKEEIEKAQVSGQGDSLHEQIADLAGSPAIKKGIL QTVKIVDELVKVMGHKPENIVIEMARENQTTTKGLQQSRERKKRIEEGIKELE SQILKENPVENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDYDVDHIVP QSFIKDDSIDNKVLTRSVENRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQ RKFDNLTKAERGGLSEADKAGFIKRQLVETRQITKHVARILDSRMNTKRDKN DKPIREVKVITLKSKLVSDFRKDFQLYKVRDINNYHHAHDAYLNAVVGTALIK KYPKLESEFVYGDYKVYDVRKMIAKSEQEIGKATAKRFFYSNIMNFFKTEVKL ANGEIRKRPLIETNGETGEVVWNKEKDFATVRKVLAMPQVNIVKKTEVQTG GFSKESILSKRESAKLIPRKKGWDTRKYGGFGSPTVAYSILVVAKVEKGKAKKL KSVKVLVGITIMEKGSYEKDPIGFLEAKGYKDIKKELIFKLPKYSLFELENGRRR MLASAKELQKANELVLPQHLVRLLYYTQNISATTGSNNLGYIEQHREEFKEIF EKIIDFSEKYILKNKVNSNLKSSFDEQFAVSDSILLSNSFVSLLKYTSFGASGGFT FLDLDVKQGRLRYQTVTEVLDATLIYQSITGLYETRTDLSQLGGD SpyCas9-3var-NRRH Streptococcus pyogenes MDKKYSIGLDIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLF 9,024 N863A H840A D10A DSGETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFL VEEDKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLALAH MIKFRGHFLIEGDLNPDNSDVDKLFIQLVQTYNQLFEENPINASGVDAKAILS ARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGLTPNFKSNFDLAEDAKLQLS KDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILLSDILRVNTEITKAPLSAS MVKRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSKNGYAGYIDGGASQEE FYKFIKPILEKMDGTEELLVKLNREDLLRKQRTFDNGIIPHQIHLGELHAILRRQ GDFYPFLKDNREKIEKILTFRIPYYVGPLARGNSRFAWMTRKSEETITPWNFE EVVDKGASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYFTVYNELTKVKYVTE GMRKPAFLSGEQKKAIVDLLFKTNRKVTVKQLKEDYFKKIECFDSVEISGVED RFNASLGTYHDLLKIIKDKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYA HLFDDKVMKQLKRLRYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANRN FMQLIHDDSLTFKEDIQKAQVSGQGDSLHEHIANLAGSPAIKKGILQTVKVV DELVKVMGGHKPENIVIEMARENQTTQKGQKNSRERMKRIEEGIKELGSQI LKEHPVENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDYDVDHIVPQSF LKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQRKF DNLTKAERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLI REVKVITLKSKLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPK LESEFVYGDYKVYDVRKMIAKSEQEIGKATAKYFFYSNIMNFFKTEITLANGEI RKRPLIETNGETGEIVWDKGRDFATVRKVLSMPQVNIVKKTEVQTGGFSKES ILPKGNSDKLIARKKDWDPKKYGGFNSPTAAYSVLVVAKVEKGKSKKLKSVK ELLGITIMERSSFEKNPIGFLEAKGYKEVKKDLIIKLPKYSLFELENGRKRMLAS AGVLHKGNELALPSKYVNFLYLASHYEKLKGSPEDNEQKQLFVEQHKHYLDE IIEQISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENIIHLFTLTNLGVPAA FKYFDTTIDKKRYTSTKEVLDATLIHQSITGLYETRIDLSQLGGD SpyCas9-3var-NRTH Streptococcus pyogenes MDKKYSIGLDIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLF 9,025 N863A H840A D10A DSGETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFL VEEDKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLALAH MIKFRGHFLIEGDLNPDNSDVDKLFIQLVQTYNQLFEENPINASGVDAKAILS ARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGLTPNFKSNFDLAEDAKLQLS KDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILLSDILRVNTEITKAPLSAS MVKRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSKNGYAGYIDGGASQEE FYKFIKPILEKMDGTEELLVKLNREDLLRKQRTFDNGIIPHQIHLGELHAILRRQ GDFYPFLKDNREKIEKILTFRIPYYVGPLARGNSRFAWMTRKSEETITPWNFE EVVDKGASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYFTVYNELTKVKYVTE GMRKPAFLSGEQKKAIVDLLFKTNRKVTVKQLKEDYFKKIECFDSVEISGVED RFNASLGTYHDLLKIIKDKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYA HLFDDKVMKQLKRLRYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANRN FMQLIHDDSLTFKEDIQKAQVSGQGDSLHEHIANLAGSPAIKKGILQTVKVV DELVKVMGGHKPENIVIEMARENQTTQKGQKNSRERMKRIEEGIKELGSQI LKEHPVENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDYDVDHIVPQSF LKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQRKF DNLTKAERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLI REVKVITLKSKLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPK LESEFVYGDYKVYDVRKMIAKSEQEIGKATAKYFFYSNIMNFFKTEITLANGEI RKRPLIETNGETGEIVWDKGRDFATVRKVLSMPQVNIVKKTEVQTGGFSKES ILPKGNSDKLIARKKDWDPKKYGGFNSPTVAYSVLVVAKVEKGKSKKLKSVK ELLGITIMERSSFEKNPIGFLEAKGYKEVKKDLIIKLPKYSLFELENGRKRMLAS ASVLHKGNELALPSKYVNFLYLASHYEKLKGSSEDNKQKQLFVEQHKHYLDEI IEQISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENIIHLFTLTNLGASAAF KYFDTTIGRKLYTSTKEVLDATLIHQSITGLYETRIDLSQLGGD SpyCas9-3var-NRCH Streptococcus pyogenes MDKKYSIGLDIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLF 9,026 N863A H840A D10A DSGETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFL VEEDKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLALAH MIKFRGHFLIEGDLNPDNSDVDKLFIQLVQTYNQLFEENPINASGVDAKAILS ARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGLTPNFKSNFDLAEDAKLQLS KDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILLSDILRVNTEITKAPLSAS MVKRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSKNGYAGYIDGGASQEE FYKFIKPILEKMDGTEELLVKLNREDLLRKQRTFDNGIIPHQIHLGELHAILRRQ GDFYPFLKDNREKIEKILTFRIPYYVGPLARGNSRFAWMTRKSEETITPWNFE EVVDKGASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYFTVYNELTKVKYVTE GMRKPAFLSGEQKKAIVDLLFKTNRKVTVKQLKEDYFKKIECFDSVEISGVED RFNASLGTYHDLLKIIKDKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYA HLFDDKVMKQLKRLRYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANRN FMQLIHDDSLTFKEDIQKAQVSGQGDSLHEHIANLAGSPAIKKGILQTVKVV DELVKVMGGHKPENIVIEMARENQTTQKGQKNSRERMKRIEEGIKELGSQI LKEHPVENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDYDVDHIVPQSF LKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQRKF DNLTKAERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLI REVKVITLKSKLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPK LESEFVYGDYKVYDVRKMIAKSEQEIGKATAKYFFYSNIMNFFKTEITLANGEI RKRPLIETNGETGEIVWDKGRDFATVRKVLSMPQVNIVKKTEVQTGGFSKES ILPKGNSDKLIARKKDWDPKKYGGFNSPTVAYSVLVVAKVEKGKSKKLKSVK ELLGITIMERSSFEKNPIDFLEAKGYKEVKKDLIIKLPKYSLFELENGRKRMLAS AGVLQKGNELALPSKYVNFLYLASHYEKLKGSPEDNEQKQLFVEQHKHYLDE IIEQISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENIIHLFTLTNLGAPAA FKYFDTTINRKQYNTTKEVLDATLIRQSITGLYETRIDLSQLGGD SpyCas9-HF1 Streptococcus pyogenes MDKKYSIGLDIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLF 9,027 N863A H840A D10A DSGETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFL VEEDKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLALAH MIKFRGHFLIEGDLNPDNSDVDKLFIQLVQTYNQLFEENPINASGVDAKAILS ARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGLTPNFKSNFDLAEDAKLQLS KDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILLSDILRVNTEITKAPLSAS MIKRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSKNGYAGYIDGGASQEEF YKFIKPILEKMDGTEELLVKLNREDLLRKQRTFDNGSIPHQIHLGELHAILRRQ EDFYPFLKDNREKIEKILTFRIPYYVGPLARGNSRFAWMTRKSEETITPWNFE EVVDKGASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYFTVYNELTKVKYVTE GMRKPAFLSGEQKKAIVDLLFKTNRKVTVKQLKEDYFKKIECFDSVEISGVED RFNASLGTYHDLLKIIKDKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYA HLFDDKVMKQLKRRRYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANR NFMQLIHDDSLTFKEDIQKAQVSGQGDSLHEHIANLAGSPAIKKGILQTVKV VDELVKVMGRHKPENIVIEMARENQTTQKGQKNSRERMKRIEEGIKELGSQ ILKEHPVENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDYDVDHIVPQSF LKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQRKF DNLTKAERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLI REVKVITLKSKLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPK LESEFVYGDYKVYDVRKMIAKSEQEIGKATAKYFFYSNIMNFFKTEITLANGEI RKRPLIETNGETGEIVWDKGRDFATVRKVLSMPQVNIVKKTEVQTGGFSKES ILPKRNSDKLIARKKDWDPKKYGGFDSPTVAYSVLVVAKVEKGKSKKLKSVKE LLGITIMERSSFEKNPIDFLEAKGYKEVKKDLIIKLPKYSLFELENGRKRMLASA GELQKGNELALPSKYVNFLYLASHYEKLKGSPEDNEQKQLFVEQHKHYLDEII EQISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENIIHLFTLTNLGAPAAF KYFDTTIDRKRYTSTKEVLDATLIHQSITGLYETRIDLSQLGGD SpyCas9-QQR1 Streptococcus pyogenes MDKKYSIGLDIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLF 9,028 N863A H840A D10A DSGETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFL VEEDKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLALAH MIKFRGHFLIEGDLNPDNSDVDKLFIQLVQTYNQLFEENPINASGVDAKAILS ARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGLTPNFKSNFDLAEDAKLQLS KDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILLSDILRVNTEITKAPLSAS MIKRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSKNGYAGYIDGGASQEEF YKFIKPILEKMDGTEELLVKLNREDLLRKQRTFDNGSIPHQIHLGELHAILRRQ EDFYPFLKDNREKIEKILTFRIPYYVGPLARGNSRFAWMTRKSEETITPWNFE EVVDKGASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYFTVYNELTKVKYVTE GMRKPAFLSGEQKKAIVDLLFKTNRKVTVKQLKEDYFKKIECFDSVEISGVED RFNASLGTYHDLLKIIKDKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYA HLFDDKVMKQLKRRRYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANR NFMQLIHDDSLTFKEDIQKAQVSGQGDSLHEHIANLAGSPAIKKGILQTVKV VDELVKVMGRHKPENIVIEMARENQTTQKGQKNSRERMKRIEEGIKELGSQ ILKEHPVENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDYDVDHIVPQSF LKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQRKF DNLTKAERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLI REVKVITLKSKLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPK LESEFVYGDYKVYDVRKMIAKSEQEIGKATAKYFFYSNIMNFFKTEITLANGEI RKRPLIETNGETGEIVWDKGRDFATVRKVLSMPQVNIVKKTEVQTGGFSKES ILPKRNSDKLIARKKDWDPKKYGGFDSPTVAYSVLVVAKVEKGKSKKLKSVKE LLGITIMERSSFEKNPIDFLEAKGYKEVKKDLIIKLPKYSLFELENGRKRMLASA RELQKGNELALPSKYVNFLYLASHYEKLKGSPEDNEQKQLFVEQHKHYLDEII EQISEFSKRVILADAQLDKVLSAYNKHRDKPIREQAENIIHLFTLTNLGAPAAF KYFDTTFKQKQYRSTKEVLDATLIHQSITGLYETRIDLSQLGGD SpyCas9-SpG Streptococcus pyogenes MDKKYSIGLDIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLF 9,029 N863A H840A D10A DSGETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFL VEEDKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLALAH MIKFRGHFLIEGDLNPDNSDVDKLFIQLVQTYNQLFEENPINASGVDAKAILS ARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGLTPNFKSNFDLAEDAKLQLS KDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILLSDILRVNTEITKAPLSAS MIKRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSKNGYAGYIDGGASQEEF YKFIKPILEKMDGTEELLVKLNREDLLRKQRTFDNGSIPHQIHLGELHAILRRQ EDFYPFLKDNREKIEKILTFRIPYYVGPLARGNSRFAWMTRKSEETITPWNFE EVVDKGASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYFTVYNELTKVKYVTE GMRKPAFLSGEQKKAIVDLLFKTNRKVTVKQLKEDYFKKIECFDSVEISGVED RFNASLGTYHDLLKIIKDKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYA HLFDDKVMKQLKRRRYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANR NFMQLIHDDSLTFKEDIQKAQVSGQGDSLHEHIANLAGSPAIKKGILQTVKV VDELVKVMGRHKPENIVIEMARENQTTQKGQKNSRERMKRIEEGIKELGSQ ILKEHPVENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDYDVDHIVPQSF LKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQRKF DNLTKAERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLI REVKVITLKSKLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPK LESEFVYGDYKVYDVRKMIAKSEQEIGKATAKYFFYSNIMNFFKTEITLANGEI RKRPLIETNGETGEIVWDKGRDFATVRKVLSMPQVNIVKKTEVQTGGFSKES ILPKRNSDKLIARKKDWDPKKYGGFLWPTVAYSVLVVAKVEKGKSKKLKSVK ELLGITIMERSSFEKNPIDFLEAKGYKEVKKDLIIKLPKYSLFELENGRKRMLAS AKQLQKGNELALPSKYVNFLYLASHYEKLKGSPEDNEQKQLFVEQHKHYLDE IIEQISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENIIHLFTLTNLGAPAA FKYFDTTIDRKQYRSTKEVLDATLIHQSITGLYETRIDLSQLGGD SpyCas9-VQR Streptococcus pyogenes MDKKYSIGLDIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLF 9,030 N863A H840A D10A DSGETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFL VEEDKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLALAH MIKFRGHFLIEGDLNPDNSDVDKLFIQLVQTYNQLFEENPINASGVDAKAILS ARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGLTPNFKSNFDLAEDAKLQLS KDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILLSDILRVNTEITKAPLSAS MIKRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSKNGYAGYIDGGASQEEF YKFIKPILEKMDGTEELLVKLNREDLLRKQRTFDNGSIPHQIHLGELHAILRRQ EDFYPFLKDNREKIEKILTFRIPYYVGPLARGNSRFAWMTRKSEETITPWNFE EVVDKGASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYFTVYNELTKVKYVTE GMRKPAFLSGEQKKAIVDLLFKTNRKVTVKQLKEDYFKKIECFDSVEISGVED RFNASLGTYHDLLKIIKDKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYA HLFDDKVMKQLKRRRYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANR NFMQLIHDDSLTFKEDIQKAQVSGQGDSLHEHIANLAGSPAIKKGILQTVKV VDELVKVMGRHKPENIVIEMARENQTTQKGQKNSRERMKRIEEGIKELGSQ ILKEHPVENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDYDVDHIVPQSF LKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQRKF DNLTKAERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLI REVKVITLKSKLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPK LESEFVYGDYKVYDVRKMIAKSEQEIGKATAKYFFYSNIMNFFKTEITLANGEI RKRPLIETNGETGEIVWDKGRDFATVRKVLSMPQVNIVKKTEVQTGGFSKES ILPKRNSDKLIARKKDWDPKKYGGFVSPTVAYSVLVVAKVEKGKSKKLKSVKE LLGITIMERSSFEKNPIDFLEAKGYKEVKKDLIIKLPKYSLFELENGRKRMLASA GELQKGNELALPSKYVNFLYLASHYEKLKGSPEDNEQKQLFVEQHKHYLDEII EQISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENIIHLFTLTNLGAPAAF KYFDTTIDRKQYRSTKEVLDATLIHQSITGLYETRIDLSQLGGD SpyCas9-VRER Streptococcus pyogenes MDKKYSIGLDIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLF 9,031 N863A H840A D10A DSGETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFL VEEDKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLALAH MIKFRGHFLIEGDLNPDNSDVDKLFIQLVQTYNQLFEENPINASGVDAKAILS ARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGLTPNFKSNFDLAEDAKLQLS KDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILLSDILRVNTEITKAPLSAS MIKRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSKNGYAGYIDGGASQEEF YKFIKPILEKMDGTEELLVKLNREDLLRKQRTFDNGSIPHQIHLGELHAILRRQ EDFYPFLKDNREKIEKILTFRIPYYVGPLARGNSRFAWMTRKSEETITPWNFE EVVDKGASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYFTVYNELTKVKYVTE GMRKPAFLSGEQKKAIVDLLFKTNRKVTVKQLKEDYFKKIECFDSVEISGVED RFNASLGTYHDLLKIIKDKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYA HLFDDKVMKQLKRRRYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANR NFMQLIHDDSLTFKEDIQKAQVSGQGDSLHEHIANLAGSPAIKKGILQTVKV VDELVKVMGRHKPENIVIEMARENQTTQKGQKNSRERMKRIEEGIKELGSQ ILKEHPVENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDYDVDHIVPQSF LKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQRKF DNLTKAERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLI REVKVITLKSKLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPK LESEFVYGDYKVYDVRKMIAKSEQEIGKATAKYFFYSNIMNFFKTEITLANGEI RKRPLIETNGETGEIVWDKGRDFATVRKVLSMPQVNIVKKTEVQTGGFSKES ILPKRNSDKLIARKKDWDPKKYGGFVSPTVAYSVLVVAKVEKGKSKKLKSVKE LLGITIMERSSFEKNPIDFLEAKGYKEVKKDLIIKLPKYSLFELENGRKRMLASA RELQKGNELALPSKYVNFLYLASHYEKLKGSPEDNEQKQLFVEQHKHYLDEII EQISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENIIHLFTLTNLGAPAAF KYFDTTIDRKEYRSTKEVLDATLIHQSITGLYETRIDLSQLGGD SpyCas9-xCas Streptococcus pyogenes MDKKYSIGLDIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLF 9,032 N863A H840A D10A DSGETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFL VEEDKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLALAH MIKFRGHFLIEGDLNPDNSDVDKLFIQLVQTYNQLFEENPINASGVDAKAILS ARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGLTPNFKSNFDLAEDTKLQLS KDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILLSDILRVNTEITKAPLSAS MIKLYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSKNGYAGYIDGGASQEEF YKFIKPILEKMDGTEELLVKLNREDLLRKQRTFDNGIIPHQIHLGELHAILRRQE DFYPFLKDNREKIEKILTFRIPYYVGPLARGNSRFAWMTRKSEETITPWNFEK VVDKGASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYFTVYNELTKVKYVTE GMRKPAFLSGDQKKAIVDLLFKTNRKVTVKQLKEDYFKKIECFDSVEISGVED RFNASLGTYHDLLKIIKDKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYA HLFDDKVMKQLKRRRYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANR NFIQLIHDDSLTFKEDIQKAQVSGQGDSLHEHIANLAGSPAIKKGILQTVKVV DELVKVMGRHKPENIVIEMARENQTTQKGQKNSRERMKRIEEGIKELGSQI LKEHPVENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDYDVDHIVPQSF LKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQRKF DNLTKAERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLI REVKVITLKSKLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPK LESEFVYGDYKVYDVRKMIAKSEQEIGKATAKYFFYSNIMNFFKTEITLANGEI RKRPLIETNGETGEIVWDKGRDFATVRKVLSMPQVNIVKKTEVQTGGFSKES ILPKRNSDKLIARKKDWDPKKYGGFDSPTVAYSVLVVAKVEKGKSKKLKSVKE LLGITIMERSSFEKNPIDFLEAKGYKEVKKDLIIKLPKYSLFELENGRKRMLASA GVLQKGNELALPSKYVNFLYLASHYEKLKGSPEDNEQKQLFVEQHKHYLDEII EQISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENIIHLFTLTNLGAPAAF KYFDTTIDRKRYTSTKEVLDATLIHQSITGLYETRIDLSQLGGD SpyCas9-xCas-NG Streptococcus pyogenes MDKKYSIGLDIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLF 9,033 N863A H840A D10A DSGETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFL VEEDKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLALAH MIKFRGHFLIEGDLNPDNSDVDKLFIQLVQTYNQLFEENPINASGVDAKAILS ARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGLTPNFKSNFDLAEDTKLQLS KDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILLSDILRVNTEITKAPLSAS MIKLYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSKNGYAGYIDGGASQEEF YKFIKPILEKMDGTEELLVKLNREDLLRKQRTFDNGIIPHQIHLGELHAILRRQE DFYPFLKDNREKIEKILTFRIPYYVGPLARGNSRFAWMTRKSEETITPWNFEK VVDKGASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYFTVYNELTKVKYVTE GMRKPAFLSGDQKKAIVDLLFKTNRKVTVKQLKEDYFKKIECFDSVEISGVED RFNASLGTYHDLLKIIKDKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYA HLFDDKVMKQLKRRRYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANR NFIQLIHDDSLTFKEDIQKAQVSGQGDSLHEHIANLAGSPAIKKGILQTVKVV DELVKVMGRHKPENIVIEMARENQTTQKGQKNSRERMKRIEEGIKELGSQI LKEHPVENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDYDVDHIVPQSF LKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQRKF DNLTKAERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLI REVKVITLKSKLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPK LESEFVYGDYKVYDVRKMIAKSEQEIGKATAKYFFYSNIMNFFKTEITLANGEI RKRPLIETNGETGEIVWDKGRDFATVRKVLSMPQVNIVKKTEVQTGGFSKES IRPKRNSDKLIARKKDWDPKKYGGFVSPTVAYSVLVVAKVEKGKSKKLKSVKE LLGITIMERSSFEKNPIDFLEAKGYKEVKKDLIIKLPKYSLFELENGRKRMLASA RFLQKGNELALPSKYVNFLYLASHYEKLKGSPEDNEQKQLFVEQHKHYLDEII EQISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENIIHLFTLTNLGAPRAF KYFDTTIDRKVYRSTKEVLDATLIHQSITGLYETRIDLSQLGGD St1Cas9-CNRZ1066 Streptococcus thermophilus MSDLVLGLDIGIGSVGVGILNKVTGEIIHKNSRIFPAAQAENNLVRRTNRQG 9,034 N622A H599A D9A RRLARRKKHRRVRLNRLFEESGLITDFTKISINLNPYQLRVKGLTDELSNEELFI ALKNMVKHRGISYLDDASDDGNSSVGDYAQIVKENSKQLETKTPGQIQLER YQTYGQLRGDFTVEKDGKKHRLINVFPTSAYRSEALRILQTQQEFNPQITDEF INRYLEILTGKRKYYHGPGNEKSRTDYGRYRTSGETLDNIFGILIGKCTFYPDEF RAAKASYTAQEFNLLNDLNNLTVPTETKKLSKEQKNQIINYVKNEKAMGPAK LFKYIAKLLSCDVADIKGYRIDKSGKAEIHTFEAYRKMKTLETLDIEQMDRETL DKLAYVLTLNTEREGIQEALEHEFADGSFSQKQVDELVQFRKANSSIFGKGW HNFSVKLMMELIPELYETSEEQMTILTRLGKQKTTSSSNKTKYIDEKLLTEEIY NPVVAKSVRQAIKIVNAAIKEYGDFDNIVIEMARETNEDDEKKAIQKIQKAN KDEKDAAMLKAANQYNGKAELPHSVFHGHKQLATKIRLWHQQGERCLYT GKTISIHDLINNSNQFEVDHILPLSITFDDSLANKVLVYATANQEKGQRTPYQ ALDSMDDAWSFRELKAFVRESKTLSNKKKEYLLTEEDISKFDVRKKFIERNLV DTRYASRVVLNALQEHFRAHKIDTKVSVVRGQFTSQLRRHWGIEKTRDTYH HHAVDALIIAASSQLNLWKKQKNTLVSYSEEQLLDIETGELISDDEYKESVFKA PYQHFVDTLKSKEFEDSILFSYQVDSKFNRKISDATIYATRQAKVGKDKKDET YVLGKIKDIYTQDGYDAFMKIYKKDKSKFLMYRHDPQTFEKVIEPILENYPNK QMNEKGKEVPCNPFLKYKEEHGYIRKYSKKGNGPEIKSLKYYDSKLLGNPIDI TPENSKNKVVLQSLKPWRTDVYFNKATGKYEILGLKYADLQFEKGTGTYKIS QEKYNDIKKKEGVDSDSEFKFTLYKNDLLLVKDTETKEQQLFRFLSRTLPKQK HYVELKPYDKQKFEGGEALIKVLGNVANGGQCIKGLAKSNISIYKVRTDVLG NQHIIKNEGDKPKLDF St1Cas9-LMG1831 Streptococcus thermophilus MSDLVLGLDIGIGSVGVGILNKVTGEIIHKNSRIFPAAQAENNLVRRTNRQG 9,035 N622A H599A D9A RRLARRKKHRRVRLNRLFEESGLITDFTKISINLNPYQLRVKGLTDELSNEELFI ALKNMVKHRGISYLDDASDDGNSSVGDYAQIVKENSKQLETKTPGQIQLER YQTYGQLRGDFTVEKDGKKHRLINVFPTSAYRSEALRILQTQQEFNPQITDEF INRYLEILTGKRKYYHGPGNEKSRTDYGRYRTSGETLDNIFGILIGKCTFYPDEF RAAKASYTAQEFNLLNDLNNLTVPTETKKLSKEQKNQIINYVKNEKAMGPAK LFKYIAKLLSCDVADIKGYRIDKSGKAEIHTFEAYRKMKTLETLDIEQMDRETL DKLAYVLTLNTEREGIQEALEHEFADGSFSQKQVDELVQFRKANSSIFGKGW HNFSVKLMMELIPELYETSEEQMTILTRLGKQKTTSSSNKTKYIDEKLLTEEIY NPVVAKSVRQAIKIVNAAIKEYGDFDNIVIEMARETNEDDEKKAIQKIQKAN KDEKDAAMLKAANQYNGKAELPHSVFHGHKQLATKIRLWHQQGERCLYT GKTISIHDLINNSNQFEVDHILPLSITFDDSLANKVLVYATANQEKGQRTPYQ ALDSMDDAWSFRELKAFVRESKTLSNKKKEYLLTEEDISKFDVRKKFIERNLV DTRYASRVVLNALQEHFRAHKIDTKVSVVRGQFTSQLRRHWGIEKTRDTYH HHAVDALIIAASSQLNLWKKQKNTLVSYSEEQLLDIETGELISDDEYKESVFKA PYQHFVDTLKSKEFEDSILFSYQVDSKFNRKISDATIYATRQAKVGKDKKDET YVLGKIKDIYTQDGYDAFMKIYKKDKSKFLMYRHDPQTFEKVIEPILENYPNK QMNEKGKEVPCNPFLKYKEEHGYIRKYSKKGNGPEIKSLKYYDSKLLGNPIDI TPENSKNKVVLQSLKPWRTDVYFNKNTGKYEILGLKYADLQFEKKTGTYKISQ EKYNGIMKEEGVDSDSEFKFTLYKNDLLLVKDTETKEQQLFRFLSRTMPNVK YYVELKPYSKDKFEKNESLIEILGSADKSGRCIKGLGKSNISIYKVRTDVLGNQH IIKNEGDKPKLDF St1Cas9-MTH17CL396 Streptococcus thermophilus MSDLVLGLDIGIGSVGVGILNKVTGEIIHKNSRIFPAAQAENNLVRRTNRQG 9,036 N622A H599A D9A RRLARRKKHRRVRLNRLFEESGLITDFTKISINLNPYQLRVKGLTDELSNEELFI ALKNMVKHRGISYLDDASDDGNSSVGDYAQIVKENSKQLETKTPGQIQLER YQTYGQLRGDFTVEKDGKKHRLINVFPTSAYRSEALRILQTQQEFNPQITDEF INRYLEILTGKRKYYHGPGNEKSRTDYGRYRTSGETLDNIFGILIGKCTFYPDEF RAAKASYTAQEFNLLNDLNNLTVPTETKKLSKEQKNQIINYVKNEKAMGPAK LFKYIAKLLSCDVADIKGYRIDKSGKAEIHTFEAYRKMKTLETLDIEQMDRETL DKLAYVLTLNTEREGIQEALEHEFADGSFSQKQVDELVQFRKANSSIFGKGW HNFSVKLMMELIPELYETSEEQMTILTRLGKQKTTSSSNKTKYIDEKLLTEEIY NPVVAKSVRQAIKIVNAAIKEYGDFDNIVIEMARETNEDDEKKAIQKIQKAN KDEKDAAMLKAANQYNGKAELPHSVFHGHKQLATKIRLWHQQGERCLYT GKTISIHDLINNSNQFEVDHILPLSITFDDSLANKVLVYATANQEKGQRTPYQ ALDSMDDAWSFRELKAFVRESKTLSNKKKEYLLTEEDISKFDVRKKFIERNLV DTRYASRVVLNALQEHFRAHKIDTKVSVVRGQFTSQLRRHWGIEKTRDTYH HHAVDALIIAASSQLNLWKKQKNTLVSYSEDQLLDIETGELISDDEYKESVFK APYQHFVDTLKSKEFEDSILFSYQVDSKFNRKISDATIYATRQAKVGKDKADE TYVLGKIKDIYTQDGYDAFMKIYKKDKSKFLMYRHDPQTFEKVIEPILENYPN KQINEKGKEVPCNPFLKYKEEHGYIRKYSKKGNGPEIKSLKYYDSKLGNHIDIT PKDSNNKVVLQSLKPWRTDVYFNKNTGKYEILGLKYSDMQFEKGTGKYSISK EQYENIKVREGVDENSEFKFTLYKNDLLLLKDSENGEQILLRFTSRNDTSKHYV ELKPYNRQKFEGSEYLIKSLGTVAKGGQCIKGLGKSNISIYKVRTDVLGNQHII KNEGDKPKLDF St1Cas9-TH1477 Streptococcus thermophilus MSDLVLGLDIGIGSVGVGILNKVTGEIIHKNSRIFPAAQAENNLVRRTNRQG 9,037 N622A H599A D9A RRLARRKKHRRVRLNRLFEESGLITDFTKISINLNPYQLRVKGLTDELSNEELFI ALKNMVKHRGISYLDDASDDGNSSVGDYAQIVKENSKQLETKTPGQIQLER YQTYGQLRGDFTVEKDGKKHRLINVFPTSAYRSEALRILQTQQEFNPQITDEF INRYLEILTGKRKYYHGPGNEKSRTDYGRYRTSGETLDNIFGILIGKCTFYPDEF RAAKASYTAQEFNLLNDLNNLTVPTETKKLSKEQKNQIINYVKNEKAMGPAK LFKYIAKLLSCDVADIKGYRIDKSGKAEIHTFEAYRKMKTLETLDIEQMDRETL DKLAYVLTLNTEREGIQEALEHEFADGSFSQKQVDELVQFRKANSSIFGKGW HNFSVKLMMELIPELYETSEEQMTILTRLGKQKTTSSSNKTKYIDEKLLTEEIY NPVVAKSVRQAIKIVNAAIKEYGDFDNIVIEMARETNEDDEKKAIQKIQKAN KDEKDAAMLKAANQYNGKAELPHSVFHGHKQLATKIRLWHQQGERCLYT GKTISIHDLINNSNQFEVDHILPLSITFDDSLANKVLVYATANQEKGQRTPYQ ALDSMDDAWSFRELKAFVRESKTLSNKKKEYLLTEEDISKFDVRKKFIERNLV DTRYASRVVLNALQEHFRAHKIDTKVSVVRGQFTSQLRRHWGIEKTRDTYH HHAVDALIIAASSQLNLWKKQKNTLVSYSEDQLLDIETGELISDDEYKESVFK APYQHFVDTLKSKEFEDSILFSYQVDSKFNRKISDATIYATRQAKVGKDKADE TYVLGKIKDIYTQDGYDAFMKIYKKDKSKFLMYRHDPQTFEKVIEPILENYPN KQINEKGKEVPCNPFLKYKEEHGYIRKYSKKGNGPEIKSLKYYDSKLGNHIDIT PKDSNNKVVLQSLKPWRTDVYFNKNTGKYEILGLKYSDMQFEKGTGKYSISK EQYENIKVREGVDENSEFKFTLYKNDLLLLKDSENGEQILLRFTSRNDTSKHYV ELKPYNRQKFEGSEYLIKSLGTVVKGGRCIKGLGKSNISIYKVRTDVLGNQHIIK NEGDKPKLDF SRGN3.1 Staphylococcus spp. MNQKFILGLDIGITSVGYGLIDYETKNIIDAGVRLFPEANVENNEGRRSKRGS 9,038 N585A H562A D10A RRLKRRRIHRLERVKLLLTEYDLINKEQIPTSNNPYQIRVKGLSEILSKDELAIAL LHLAKRRGIHNVDVAADKEETASDSLSTKDQINKNAKFLESRYVCELQKERLE NEGHVRGVENRFLTKDIVREAKKIIDTQMQYYPEIDETFKEKYISLVETRREYF EGPGQGSPFGWNGDLKKWYEMLMGHCTYFPQELRSVKYAYSADLFNALN DLNNLIIQRDNSEKLEYHEKYHIIENVFKQKKKPTLKQIAKEIGVNPEDIKGYRI TKSGTPEFTSFKLFHDLKKVVKDHAILDDIDLLNQIAEILTIYQDKDSIVAELGQ LEYLMSEADKQSISELTGYTGTHSLSLKCMNMIIDELWHSSMNQMEVFTYL NMRPKKYELKGYQRIPTDMIDDAILSPVVKRTFIQSINVINKVIEKYGIPEDIIIE LARENNSDDRKKFINNLQKKNEATRKRINEIIGQTGNQNAKRIVEKIRLHDQ QEGKCLYSLESIPLEDLLNNPNHYEVDHIIPRSVSFDNSYHNKVLVKQSENSK KSNLTPYQYFNSGKSKLSYNQFKQHILNLSKSQDRISKKKKEYLLEERDINKFE VQKEFINRNLVDTRYATRELTNYLKAYFSANNMNVKVKTINGSFTDYLRKV WKFKKERNHGYKHHAEDALIIANADFLFKENKKLKAVNSVLEKPEIETKQLDI QVDSEDNYSEMFIIPKQVQDIKDFRNFKYSHRVDKKPNRQLINDTLYSTRKK DNSTYIVQTIKDIYAKDNTTLKKQFDKSPEKFLMYQHDPRTFEKLEVIMKQYA NEKNPLAKYHEETGEYLTKYSKKNNGPIVKSLKYIGNKLGSHLDVTHQFKSST KKLVKLSIKNYRFDVYLTEKGYKFVTIAYLNVFKKDNYYYIPKDKYQELKEKKKI KDTDQFIASFYKNDLIKLNGDLYKIIGVNSDDRNIIELDYYDIKYKDYCEINNIK GEPRIKKTIGKKTESIEKFTTDVLGNLYLHSTEKAPQLIFKRGL SRGN3.3 Staphylococcus spp. MNQKFILGLDIGITSVGYGLIDYETKNIIDAGVRLFPEANVENNEGRRSKRGS 9,039 N585A H562A D10A RRLKRRRIHRLERVKLLLTEYDLINKEQIPTSNNPYQIRVKGLSEILSKDELAIAL LHLAKRRGIHNVDVAADKEETASDSLSTKDQINKNAKFLESRYVCELQKERLE NEGHVRGVENRFLTKDIVREAKKIIDTQMQYYPEIDETFKEKYISLVETRREYF EGPGQGSPFGWNGDLKKWYEMLMGHCTYFPQELRSVKYAYSADLFNALN DLNNLIIQRDNSEKLEYHEKYHIIENVFKQKKKPTLKQIAKEIGVNPEDIKGYRI TKSGTPEFTSFKLFHDLKKVVKDHAILDDIDLLNQIAEILTIYQDKDSIVAELGQ LEYLMSEADKQSISELTGYTGTHSLSLKCMNMIIDELWHSSMNQMEVFTYL NMRPKKYELKGYQRIPTDMIDDAILSPVVKRTFIQSINVINKVIEKYGIPEDIIIE LARENNSDDRKKFINNLQKKNEATRKRINEIIGQTGNQNAKRIVEKIRLHDQ QEGKCLYSLESIPLEDLLNNPNHYEVDHIIPRSVSFDNSYHNKVLVKQSENSK KSNLTPYQYFNSGKSKLSYNQFKQHILNLSKSQDRISKKKKEYLLEERDINKFE VQKEFINRNLVDTRYATRELTSYLKAYFSANNMDVKVKTINGSFTNHLRKV WRFDKYRNHGYKHHAEDALIIANADFLFKENKKLQNTNKILEKPTIENNTKK VTVEKEEDYNNVFETPKLVEDIKQYRDYKFSHRVDKKPNRQLINDTLYSTRM KDEHDYIVQTITDIYGKDNTNLKKQFNKNPEKFLMYQNDPKTFEKLSIIMKQ YSDEKNPLAKYYEETGEYLTKYSKKNNGPIVKKIKLLGNKVGNHLDVTNKYEN STKKLVKLSIKNYRFDVYLTEKGYKFVTIAYLNVFKKDNYYYIPKDKYQELKEKK KIKDTDQFIASFYKNDLIKLNGDLYKIIGVNSDDRNIIELDYYDIKYKDYCEINNI KGEPRIKKTIGKKTESIEKFTTDVLGNLYLHSTEKAPQLIFKRGL

In some embodiments, a Cas protein requires a protospacer adjacent motif (PAM) to be present in or adjacent to a target DNA sequence for the Cas protein to bind and/or function. In some embodiments, the PAM is or comprises, from 5′ to 3′, NGG, YG, NNGRRT, NNNRRT, NGA, TYCV, TATV, NTTN, or NNNGATT, where N stands for any nucleotide, Y stands for C or T, R stands for A or G, and V stands for A or C or G. In some embodiments, a Cas protein is a protein listed in Table 7 or 8. In some embodiments, a Cas protein comprises one or more mutations altering its PAM. In some embodiments, a Cas protein comprises E1369R, E1449H, and R1556A mutations or analogous substitutions to the amino acids corresponding to said positions. In some embodiments, a Cas protein comprises E782K, N968K, and R1015H mutations or analogous substitutions to the amino acids corresponding to said positions. In some embodiments, a Cas protein comprises D1135V, R1335Q, and T1337R mutations or analogous substitutions to the amino acids corresponding to said positions. In some embodiments, a Cas protein comprises S542R and K607R mutations or analogous substitutions to the amino acids corresponding to said positions. In some embodiments, a Cas protein comprises S542R, K548V, and N552R mutations or analogous substitutions to the amino acids corresponding to said positions. Exemplary advances in the engineering of Cas enzymes to recognize altered PAM sequences are reviewed in Collias et al Nature Communications 12:555 (2021), incorporated herein by reference in its entirety.

In some embodiments, the Cas protein is catalytically active and cuts one or both strands of the target DNA site. In some embodiments, cutting the target DNA site is followed by formation of an alteration, e.g., an insertion or deletion, e.g., by the cellular repair machinery.

In some embodiments, the Cas protein is modified to deactivate or partially deactivate the nuclease, e.g., nuclease-deficient Cas9. Whereas wild-type Cas9 generates double-strand breaks (DSBs) at specific DNA sequences targeted by a gRNA, a number of CRISPR endonucleases having modified functionalities are available, for example: a “nickase” version of Cas9 that has been partially deactivated generates only a single-strand break; a catalytically inactive Cas9 (“dCas9”) does not cut target DNA. In some embodiments, dCas9 binding to a DNA sequence may interfere with transcription at that site by steric hindrance. In some embodiments, dCas9 binding to an anchor sequence may interfere with (e.g., decrease or prevent) genomic complex (e.g., ASMC) formation and/or maintenance. In some embodiments, a DNA-binding domain comprises a catalytically inactive Cas9, e.g., dCas9. Many catalytically inactive Cas9 proteins are known in the art. In some embodiments, dCas9 comprises mutations in each endonuclease domain of the Cas protein, e.g., D10A and H840A or N863A mutations. In some embodiments, a catalytically inactive or partially inactive CRISPR/Cas domain comprises a Cas protein comprising one or more mutations, e.g., one or more of the mutations listed in Table 7. In some embodiments, a Cas protein described on a given row of Table 7 comprises one, two, three, or all of the mutations listed in the same row of Table 7. In some embodiments, a Cas protein, e.g., not described in Table 7, comprises one, two, three, or all of the mutations listed in a row of Table 7 or a corresponding mutation at a corresponding site in that Cas protein.

In some embodiments, a Cas9 derivative with enhanced activity may be used in the gene modification polypeptide. In some embodiments, a Cas9 derivative may comprise mutations that improve activity of the HNH endonuclease domain, e.g., SpyCas9 R221K, N394K, or mutations that improve R-loop formation, e.g., SpyCas9 L1245V, or comprise a combination of such mutations, e.g., SpyCas9 R221K/N394K, SpyCas9 N394K/L1245V, SpyCas9 R221K/L1245V, or SpyCas9 R221K/N394K/L1245V (see, e.g., Spencer and Zhang Sci Rep 7:16836 (2017), the Cas9 derivatives and comprising mutations of which are incorporated herein by reference). In some embodiments, a Cas9 derivative may comprise one or more types of mutations described herein, e.g., PAM-modifying mutations, protein stabilizing mutations, activity enhancing mutations, and/or mutations partially or fully inactivating one or two endonuclease domains relative to the parental enzyme (e.g., one or more mutations to abolish endonuclease activity towards one or both strands of a target DNA, e.g., a nickase or catalytically dead enzyme). In some embodiments, a Cas9 enzyme used in a system described herein may comprise mutations that confer nickase activity toward the enzyme (e.g., SpyCas9 N863A or H840A) in addition to mutations improving catalytic efficiency (e.g., SpyCas9 R221K, N394K, and/or L1245V). In some embodiments, a Cas9 enzyme used in a system described herein is a SpyCas9 enzyme or derivative that further comprises an N863A mutation to confer nickase activity in addition to R221K and N394K mutations to improve catalytic efficiency.

In some embodiments, a catalytically inactive, e.g., dCas9, or partially deactivated Cas9 protein comprises a D11 mutation (e.g., D11A mutation) or an analogous substitution to the amino acid corresponding to said position. In some embodiments, a catalytically inactive Cas9 protein, e.g., dCas9, or partially deactivated Cas9 protein comprises a H969 mutation (e.g., H969A mutation) or an analogous substitution to the amino acid corresponding to said position. In some embodiments, a catalytically inactive Cas9 protein, e.g., dCas9, or partially deactivated Cas9 protein comprises a N995 mutation (e.g., N995A mutation) or an analogous substitution to the amino acid corresponding to said position. In some embodiments, a catalytically inactive Cas9 protein, e.g., dCas9, comprises mutations at one, two, or three of positions D11, H969, and N995 (e.g., D11A, H969A, and N995A mutations) or analogous substitutions to the amino acids corresponding to said positions.

In some embodiments, a catalytically inactive Cas9 protein, e.g., dCas9, or partially deactivated Cas9 protein comprises a D10 mutation (e.g., a D10A mutation) or an analogous substitution to the amino acid corresponding to said position. In some embodiments, a catalytically inactive Cas9 protein, e.g., dCas9, or partially deactivated Cas9 protein comprises a H557 mutation (e.g., a H557A mutation) or an analogous substitution to the amino acid corresponding to said position. In some embodiments, a catalytically inactive Cas9 protein, e.g., dCas9, comprises a D10 mutation (e.g., a D10A mutation) and a H557 mutation (e.g., a H557A mutation) or analogous substitutions to the amino acids corresponding to said positions.

In some embodiments, a catalytically inactive Cas9 protein, e.g., dCas9, or partially deactivated Cas9 protein comprises a D839 mutation (e.g., a D839A mutation) or an analogous substitution to the amino acid corresponding to said position. In some embodiments, a catalytically inactive Cas9 protein, e.g., dCas9, or partially deactivated Cas9 protein comprises a H840 mutation (e.g., a H840A mutation) or an analogous substitution to the amino acid corresponding to said position. In some embodiments, a catalytically inactive Cas9 protein, e.g., dCas9, or partially deactivated Cas9 protein comprises a N863 mutation (e.g., a N863A mutation) or an analogous substitution to the amino acid corresponding to said position. In some embodiments, a catalytically inactive Cas9 protein, e.g., dCas9, comprises a D10 mutation (e.g., D10A), a D839 mutation (e.g., D839A), a H840 mutation (e.g., H840A), and a N863 mutation (e.g., N863A) or analogous substitutions to the amino acids corresponding to said positions.

In some embodiments, a catalytically inactive Cas9 protein, e.g., dCas9, or partially deactivated Cas9 protein comprises a E993 mutation (e.g., a E993A mutation) or an analogous substitution to the amino acid corresponding to said position.

In some embodiments, a catalytically inactive Cas9 protein, e.g., dCas9, or partially deactivated Cas9 protein comprises a D917 mutation (e.g., a D917A mutation) or an analogous substitution to the amino acid corresponding to said position. In some embodiments, a catalytically inactive Cas9 protein, e.g., dCas9, or partially deactivated Cas9 protein comprises a E1006 mutation (e.g., a E1006A mutation) or an analogous substitution to the amino acid corresponding to said position. In some embodiments, a catalytically inactive Cas9 protein, e.g., dCas9, or partially deactivated Cas9 protein comprises a D1255 mutation (e.g., a D1255A mutation) or an analogous substitution to the amino acid corresponding to said position. In some embodiments, a catalytically inactive Cas9 protein, e.g., dCas9, comprises a D917 mutation (e.g., D917A), a E1006 mutation (e.g., E1006A), and a D1255 mutation (e.g., D1255A) or analogous substitutions to the amino acids corresponding to said positions.

In some embodiments, a catalytically inactive Cas9 protein, e.g., dCas9, or partially deactivated Cas9 protein comprises a D16 mutation (e.g., a D16A mutation) or an analogous substitution to the amino acid corresponding to said position. In some embodiments, a catalytically inactive Cas9 protein, e.g., dCas9, or partially deactivated Cas9 protein comprises a D587 mutation (e.g., a D587A mutation) or an analogous substitution to the amino acid corresponding to said position. In some embodiments, a partially deactivated Cas domain has nickase activity. In some embodiments, a partially deactivated Cas9 domain is a Cas9 nickase domain. In some embodiments, the catalytically inactive Cas domain or dead Cas domain produces no detectable double strand break formation. In some embodiments, a catalytically inactive Cas9 protein, e.g., dCas9, or partially deactivated Cas9 protein comprises a H588 mutation (e.g., a H588A mutation) or an analogous substitution to the amino acid corresponding to said position. In some embodiments, a catalytically inactive Cas9 protein, e.g., dCas9, or partially deactivated Cas9 protein comprises a N611 mutation (e.g., a N611 A mutation) or an analogous substitution to the amino acid corresponding to said position. In some embodiments, a catalytically inactive Cas9 protein, e.g., dCas9, comprises a D16 mutation (e.g., D16A), a D587 mutation (e.g., D587A), a H588 mutation (e.g., H588A), and a N611 mutation (e.g., N611A) or analogous substitutions to the amino acids corresponding to said positions.

In some embodiments, a DNA-binding domain or endonuclease domain may comprise a Cas molecule comprising or linked (e.g., covalently) to a gRNA (e.g., a template nucleic acid, e.g., template RNA, comprising a gRNA).

In some embodiments, an endonuclease domain or DNA binding domain comprises a Streptococcus pyogenes Cas9 (SpCas9) or a functional fragment or variant thereof. In some embodiments, the endonuclease domain or DNA binding domain comprises a modified SpCas9. In embodiments, the modified SpCas9 comprises a modification that alters protospacer-adjacent motif (PAM) specificity. In embodiments, the PAM has specificity for the nucleic acid sequence 5′-NGT-3′. In embodiments, the modified SpCas9 comprises one or more amino acid substitutions, e.g., at one or more of positions L1111, D1135, G1218, E1219, A1322, of R1335, e.g., selected from L1111R, D1135V, G1218R, E1219F, A1322R, R1335V. In embodiments, the modified SpCas9 comprises the amino acid substitution T1337R and one or more additional amino acid substitutions, e.g., selected from L1111, D1135L, S1136R, G1218S, E1219V, D1332A, D1332S, D1332T, D1332V, D1332L, D1332K, D1332R, R1335Q, T1337, T1337L, T1337Q, T1337I, T1337V, T1337F, T1337S, T1337N, T1337K, T1337H, T1337Q, and T1337M, or corresponding amino acid substitutions thereto. In embodiments, the modified SpCas9 comprises: (i) one or more amino acid substitutions selected from D1135L, S1136R, G1218S, E1219V, A1322R, R1335Q, and T1337; and (ii) one or more amino acid substitutions selected from L1111R, G1218R, E1219F, D1332A, D1332S, D1332T, D1332V, D1332L, D1332K, D1332R, T1337L, T1337I, T1337V, T1337F, T1337S, T1337N, T1337K, T1337R, T1337H, T1337Q, and T1337M, or corresponding amino acid substitutions thereto.

In some embodiments, the endonuclease domain or DNA binding domain comprises a Cas domain, e.g., a Cas9 domain. In embodiments, the endonuclease domain or DNA binding domain comprises a nuclease-active Cas domain, a Cas nickase (nCas) domain, or a nuclease-inactive Cas (dCas) domain. In embodiments, the endonuclease domain or DNA binding domain comprises a nuclease-active Cas9 domain, a Cas9 nickase (nCas9) domain, or a nuclease-inactive Cas9 (dCas9) domain. In some embodiments, the endonuclease domain or DNA binding domain comprises a Cas9 domain of Cas9 (e.g., dCas9 and nCas9), Cas12a/Cpf1, Cas12b/C2c1, Cas12c/C2c3, Cas12d/CasY, Cas12e/CasX, Cas12g, Cas12h, or Cas12i. In some embodiments, the endonuclease domain or DNA binding domain comprises a Cas9 (e.g., dCas9 and nCas9), Cas12a/Cpf1, Cas12b/C2c1, Cas12c/C2c3, Cas12d/CasY, Cas12e/CasX, Cas12g, Cas12h, or Cas12i. In some embodiments, the endonuclease domain or DNA binding domain comprises an S. pyogenes or an S. thermophilus Cas9, or a functional fragment thereof. In some embodiments, the endonuclease domain or DNA binding domain comprises a Cas9 sequence, e.g., as described in Chylinski, Rhun, and Charpentier (2013) RNA Biology 10:5, 726-737; incorporated herein by reference. In some embodiments, the endonuclease domain or DNA binding domain comprises the HNH nuclease subdomain and/or the RuvC1 subdomain of a Cas, e.g., Cas9, e.g., as described herein, or a variant thereof. In some embodiments, the endonuclease domain or DNA binding domain comprises Cas12a/Cpf1, Cas12b/C2c1, Cas12c/C2c3, Cas12d/CasY, Cas12e/CasX, Cas12g, Cas12h, or Cas12i. In some embodiments, the endonuclease domain or DNA binding domain comprises a Cas polypeptide (e.g., enzyme), or a functional fragment thereof. In embodiments, the Cas polypeptide (e.g., enzyme) is selected from Cas1, Cas1B, Cas2, Cas3, Cas4, Cas5, Cas5d, Cas5t, Cas5h, Cas5a, Cas6, Cas7, Cas8, Cas8a, Cas8b, Cas8c, Cas9 (e.g., Csn1 or Csx12), Cas10, Cas10d, Cas12a/Cpf1, Cas12b/C2c1, Cas12c/C2c3, Cas12d/CasY, Cas12e/CasX, Cas12g, Cas12h, Cas12i, Csy1, Csy2, Csy3, Csy4, Cse1, Cse2, Cse3, Cse4, Cse5e, Csc1, Csc2, Csa5, Csn1, Csn2, Csm1, Csm2, Csm3, Csm4, Csm5, Csm6, Cmr1, Cmr3, Cmr4, Cmr5, Cmr6, Csb1, Csb2, Csb3, Csx17, Csx14, Csx10, Csx16, CsaX, Csx3, Csx1, Csx1S, Csx11, Csf1, Csf2, CsO, Csf4, Csd1, Csd2, Cst1, Cst2, Csh1, Csh2, Csa1, Csa2, Csa3, Csa4, Csa5, Type II Cas effector proteins, Type V Cas effector proteins, Type VI Cas effector proteins, CARF, DinG, Cpf1, Cas12b/C2c1, Cas12c/C2c3, Cas12b/C2c1, Cas12c/C2c3, SpCas9 (K855A), eSpCas9 (1.1), SpCas9-HF1, hyper accurate Cas9 variant (HypaCas9), homologues thereof, modified or engineered versions thereof, and/or functional fragments thereof. In embodiments, the Cas9 comprises one or more substitutions, e.g., selected from H840A, D10A, P475A, W476A, N477A, D1125A, W1126A, and D1127A. In embodiments, the Cas9 comprises one or more mutations at positions selected from: D10, G12, G17, E762, H840, N854, N863, H982, H983, A984, D986, and/or A987, e.g., one or more substitutions selected from D10A, G12A, G17A, E762A, H840A, N854A, N863A, H982A, H983A, A984A, and/or D986A. In some embodiments, the endonuclease domain or DNA binding domain comprises a Cas (e.g., Cas9) sequence from Corynebacterium ulcerans, Corynebacterium diphtheria, Spiroplasma syrphidicola, Prevotella intermedia, Spiroplasma taiwanense, Streptococcus iniae, Belliella baltica, Psychroflexus torquis, Streptococcus thermophilus, Listeria innocua, Campylobacter jejuni, Neisseria meningitidis, Streptococcus pyogenes, or Staphylococcus aureus, or a fragment or variant thereof.

In some embodiments, the endonuclease domain or DNA binding domain comprises a Cpf1 domain, e.g., comprising one or more substitutions, e.g., at position D917, E1006A, D1255 or any combination thereof, e.g., selected from D917A, E1006A, D1255A, D917A/E1006A, D917A/D1255A, E1006A/D1255A, and D917A/E1006A/D1255A.

In some embodiments, the endonuclease domain or DNA binding domain comprises spCas9, spCas9-VRQR, spCas9−VRER, xCas9 (sp), saCas9, saCas9-KKH, spCas9-MQKSER, spCas9-LRKIQK, or spCas9-LRVSQL.

In some embodiments, a gene modifying polypeptide has an endonuclease domain comprising a Cas9 nickase, e.g., Cas9 H840A. In embodiments, the Cas9 H840A has the following amino acid sequence:

Cas9 nickase (H840A): (SEQ ID NO: 11,001) DKKYSIGLDIGTNSVGWAVITDEYKVPSKKFKVLGNTDRH SIKKNLIGALLFDSGETAEATRLKRTARRRYTRRKNRICY LQEIFSNEMAKVDDSFFHRLEESFLVEEDKKHERHPIFGN IVDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLALAHM IKFRGHFLIEGDLNPDNSDVDKLFIQLVQTYNQLFEENPI NASGVDAKAILSARLSKSRRLENLIAQLPGEKKNGLFGNL IALSLGLTPNFKSNFDLAEDAKLQLSKDTYDDDLDNLLAQ IGDQYADLFLAAKNLSDAILLSDILRVNTEITKAPLSASM IKRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSKNGYAG YIDGGASQEEFYKFIKPILEKMDGTEELLVKLNREDLLRK QRTFDNGSIPHQIHLGELHAILRRQEDFYPFLKDNREKIE KILTFRIPYYVGPLARGNSRFAWMTRKSEETITPWNFEEV VDKGASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYFTVY NELTKVKYVTEGMRKPAFLSGEQKKAIVDLLFKTNRKVTV KQLKEDYFKKIECFDSVEISGVEDRFNASLGTYHDLLKII KDKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYAH LFDDKVMKQLKRRRYTGWGRLSRKLINGIRDKQSGKTILD FLKSDGFANRNFMQLIHDDSLTFKEDIQKAQVSGQGDSLH EHIANLAGSPAIKKGILQTVKVVDELVKVMGRHKPENIVI EMARENQTTQKGQKNSRERMKRIEEGIKELGSQILKEHPV ENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDYDVDAI VPQSFLKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKN YWRQLLNAKLITQRKFDNLTKAERGGLSELDKAGFIKRQL VETRQITKHVAQILDSRMNTKYDENDKLIREVKVITLKSK LVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKY PKLESEFVYGDYKVYDVRKMIAKSEQEIGKATAKYFFYSN IMNFFKTEITLANGEIRKRPLIETNGETGEIVWDKGRDFA TVRKVLSMPQVNIVKKTEVQTGGFSKESILPKRNSDKLIA RKKDWDPKKYGGFDSPTVAYSVLVVAKVEKGKSKKLKSVK ELLGITIMERSSFEKNPIDFLEAKGYKEVKKDLIIKLPKY SLFELENGRKRMLASAGELQKGNELALPSKYVNFLYLASH YEKLKGSPEDNEQKQLFVEQHKHYLDEIIEQISEFSKRVI LADANLDKVLSAYNKHRDKPIREQAENIIHLFTLTNLGAP AAFKYFDTTIDRKRYTSTKEVLDATLIHQSITGLYETRID LSQLGGD

In some embodiments, a gene modifying polypeptide comprises a dCas9 sequence comprising a D10A and/or H840A mutation, e.g., the following sequence:

(SEQ ID NO: 5007) SMDKKYSIGLAIGTNSVGWAVITDDYKVPSKKFKVLGNTD RHSIKKNLIGALLFDSGETAEATRLKRTARRRYTRRKNRI CYLQEIFSNEMAKVDDSFFHRLEESFLVEEDKKHERHPIF GNIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLALA HMIKFRGHFLIEGDLNPDNSDVDKLFIQLVQTYNQLFEEN PINASGVDAKAILSARLSKSRRLENLIAQLPGEKKNGLFG NLIALSLGLTPNFKSNFDLAEDAKLQLSKDTYDDDLDNLL AQIGDQYADLFLAAKNLSDAILLSDILRVNTEITKAPLSA SMIKRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSKNGY AGYIDGGASQEEFYKFIKPILEKMDGTEELLVKLNREDL LRKQRTFDNGSIPHQIHLGELHAILRRQEDFYPFLKDNRE KIEKILTFRIPYYVGPLARGNSRFAWMTRKSEETITPWNF EEVVDKGASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYF TVYNELTKVKYVTEGMRKPAFLSGEQKKAIVDLLFKTNRK VTVKQLKEDYFKKIECFDSVEISGVEDRFNASLGTYHDLL KIIKDKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKT YAHLFDDKVMKQLKRRRYTGWGRLSRKLINGIRDKQSGKT ILDFLKSDGFANRNFMQLIHDDSLTFKEDIQKAQVSGQGD SLHEHIANLAGSPAIKKGILQTVKVVDELVKVMGRHKPE NIVIEMARENQTTQKGQKNSRERMKRIEEGIKELGSQILK EHPVENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDYD VDAIVPQSFLKDDSIDNKVLTRSDKNRGKSDNVPSEEVVK KMKNYWRQLLNAKLITQRKFDNLTKAERGGLSELDKAGFI KRQLVETRQITKHVAQILDSRMNTKYDENDKLIREVKVIT LKSKLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTAL IKKYPKLESEFVYGDYKVYDVRKMIAKSEQEIGKATAKYF FYSNIMNFFKTEITLANGEIRKRPLIETNGETGEIVWDKG RDFATVRKVLSMPQVNIVKKTEVQTGGFSKESILPKRNS DKLIARKKDWDPKKYGGFDSPTVAYSVLVVAKVEKGKSKK LKSVKELLGITIMERSSFEKNPIDFLEAKGYKEVKKDLII KLPKYSLFELENGRKRMLASAGELQKGNELALPSKYVNFL YLASHYEKLKGSPEDNEQKQLFVEQHKHYLDEIIEQISEF SKRVILADANLDKVLSAYNKHRDKPIREQAENIIHLFTLT NLGAPAAFKYFDTTIDRKRYTSTKEVLDATLIHQSITGLY ETRIDLSQLGGD

TAL Effectors and Zinc Finger Nucleases

In some embodiments, an endonuclease domain or DNA-binding domain comprises a TAL effector molecule. A TAL effector molecule, e.g., a TAL effector molecule that specifically binds a DNA sequence, typically comprises a plurality of TAL effector domains or fragments thereof, and optionally one or more additional portions of naturally occurring TAL effectors (e.g., N- and/or C-terminal of the plurality of TAL effector domains). Many TAL effectors are known to those of skill in the art and are commercially available, e.g., from Thermo Fisher Scientific.

Naturally occurring TALEs are natural effector proteins secreted by numerous species of bacterial pathogens including the plant pathogen Xanthomonas which modulates gene expression in host plants and facilitates bacterial colonization and survival. The specific binding of TAL effectors is based on a central repeat domain of tandemly arranged nearly identical repeats of typically 33 or 34 amino acids (the repeat-variable di-residues, RVD domain).

Members of the TAL effectors family differ mainly in the number and order of their repeats. The number of repeats typically ranges from 1.5 to 33.5 repeats and the C-terminal repeat is usually shorter in length (e.g., about 20 amino acids) and is generally referred to as a “half-repeat.” Each repeat of the TAL effector generally features a one-repeat-to-one-base-pair correlation with different repeat types exhibiting different base-pair specificity (one repeat recognizes one base-pair on the target gene sequence). Generally, the smaller the number of repeats, the weaker the protein-DNA interactions. A number of 6.5 repeats has been shown to be sufficient to activate transcription of a reporter gene (Scholze et al., 2010).

Repeat to repeat variations occur predominantly at amino acid positions 12 and 13, which have therefore been termed “hypervariable” and which are responsible for the specificity of the interaction with the target DNA promoter sequence, as shown in Table 9 listing exemplary repeat variable diresidues (RVD) and their correspondence to nucleic acid base targets.

TABLE 9 RVDs and Nucleic Acid Base Specificity Target Possible RVD Amino Acid Combinations A NI NN CI HI KI G NN GN SN VN LN DN QN EN HN RH NK AN FN C HD RD KD ND AD T NG HG VG IG EG MG YG AA EP VA QG KG RG

Accordingly, it is possible to modify the repeats of a TAL effector to target specific DNA sequences. Further studies have shown that the RVD NK can target G. Target sites of TAL effectors also tend to include a T flanking the 5′ base targeted by the first repeat, but the exact mechanism of this recognition is not known. More than 113 TAL effector sequences are known to date. Non-limiting examples of TAL effectors from Xanthomonas include, Hax2, Hax3, Hax4, AvrXa7, AvrXa10 and AvrBs3.

Accordingly, the TAL effector domain of a TAL effector molecule described herein may be derived from a TAL effector from any bacterial species (e.g., Xanthomonas species such as the African strain of Xanthomonas oryzae pv. Oryzae (Yu et al. 2011), Xanthomonas campestris pv. raphani strain 756C and Xanthomonas oryzae pv. oryzicolastrain BLS256 (Bogdanove et al. 2011). In some embodiments, the TAL effector domain comprises an RVD domain as well as flanking sequence(s) (sequences on the N-terminal and/or C-terminal side of the RVD domain) also from the naturally occurring TAL effector. It may comprise more or fewer repeats than the RVD of the naturally occurring TAL effector. The TAL effector molecule can be designed to target a given DNA sequence based on the above code and others known in the art. The number of TAL effector domains (e.g., repeats (monomers or modules)) and their specific sequence can be selected based on the desired DNA target sequence. For example, TAL effector domains, e.g., repeats, may be removed or added in order to suit a specific target sequence. In an embodiment, the TAL effector molecule of the present invention comprises between 6.5 and 33.5 TAL effector domains, e.g., repeats. In an embodiment, TAL effector molecule of the present invention comprises between 8 and 33.5 TAL effector domains, e.g., repeats, e.g., between 10 and 25 TAL effector domains, e.g., repeats, e.g., between 10 and 14 TAL effector domains, e.g., repeats.

In some embodiments, the TAL effector molecule comprises TAL effector domains that correspond to a perfect match to the DNA target sequence. In some embodiments, a mismatch between a repeat and a target base-pair on the DNA target sequence is permitted as along as it allows for the function of the polypeptide comprising the TAL effector molecule. In general, TALE binding is inversely correlated with the number of mismatches. In some embodiments, the TAL effector molecule of a polypeptide of the present invention comprises no more than 7 mismatches, 6 mismatches, 5 mismatches, 4 mismatches, 3 mismatches, 2 mismatches, or 1 mismatch, and optionally no mismatch, with the target DNA sequence. Without wishing to be bound by theory, in general the smaller the number of TAL effector domains in the TAL effector molecule, the smaller the number of mismatches will be tolerated and still allow for the function of the polypeptide comprising the TAL effector molecule. The binding affinity is thought to depend on the sum of matching repeat-DNA combinations. For example, TAL effector molecules having 25 TAL effector domains or more may be able to tolerate up to 7 mismatches.

In addition to the TAL effector domains, the TAL effector molecule of the present invention may comprise additional sequences derived from a naturally occurring TAL effector. The length of the C-terminal and/or N-terminal sequence(s) included on each side of the TAL effector domain portion of the TAL effector molecule can vary and be selected by one skilled in the art, for example based on the studies of Zhang et al. (2011). Zhang et al., have characterized a number of C-terminal and N-terminal truncation mutants in Hax3 derived TAL-effector based proteins and have identified key elements, which contribute to optimal binding to the target sequence and thus activation of transcription. Generally, it was found that transcriptional activity is inversely correlated with the length of N-terminus. Regarding the C-terminus, an important element for DNA binding residues within the first 68 amino acids of the Hax 3 sequence was identified. Accordingly, in some embodiments, the first 68 amino acids on the C-terminal side of the TAL effector domains of the naturally occurring TAL effector is included in the TAL effector molecule. Accordingly, in an embodiment, a TAL effector molecule comprises 1) one or more TAL effector domains derived from a naturally occurring TAL effector; 2) at least 70, 80, 90, 100, 110, 120, 130, 140, 150, 170, 180, 190, 200, 220, 230, 240, 250, 260, 270, 280 or more amino acids from the naturally occurring TAL effector on the N-terminal side of the TAL effector domains; and/or 3) at least 68, 80, 90, 100, 110, 120, 130, 140, 150, 170, 180, 190, 200, 220, 230, 240, 250, 260 or more amino acids from the naturally occurring TAL effector on the C-terminal side of the TAL effector domains.

In some embodiments, an endonuclease domain or DNA-binding domain is or comprises a Zn finger molecule. A Zn finger molecule comprises a Zn finger protein, e.g., a naturally occurring Zn finger protein or engineered Zn finger protein, or fragment thereof. Many Zn finger proteins are known to those of skill in the art and are commercially available, e.g., from Sigma-Aldrich.

In some embodiments, a Zn finger molecule comprises a non-naturally occurring Zn finger protein that is engineered to bind to a target DNA sequence of choice. See, for example, Beerli, et al. (2002) Nature Biotechnol. 20:135-141; Pabo, et al. (2001) Ann. Rev. Biochem. 70:313-340; Isalan, et al. (2001) Nature Biotechnol. 19:656-660; Segal, et al. (2001) Curr. Opin. Biotechnol. 12:632-637; Choo, et al. (2000) Curr. Opin. Struct. Biol. 10:411-416; U.S. Pat. Nos. 6,453,242; 6,534,261; 6,599,692; 6,503,717; 6,689,558; 7,030,215; 6,794,136; 7,067,317; 7,262,054; 7,070,934; 7,361,635; 7,253,273; and U.S. Patent Publication Nos. 2005/0064474; 2007/0218528; 2005/0267061, all incorporated herein by reference in their entireties.

An engineered Zn finger protein may have a novel binding specificity, compared to a naturally-occurring Zn finger protein. Engineering methods include, but are not limited to, rational design and various types of selection. Rational design includes, for example, using databases comprising triplet (or quadruplet) nucleotide sequences and individual Zn finger amino acid sequences, in which each triplet or quadruplet nucleotide sequence is associated with one or more amino acid sequences of zinc fingers which bind the particular triplet or quadruplet sequence. See, for example, U.S. Pat. Nos. 6,453,242 and 6,534,261, incorporated by reference herein in their entireties.

Exemplary selection methods, including phage display and two-hybrid systems, are disclosed in U.S. Pat. Nos. 5,789,538; 5,925,523; 6,007,988; 6,013,453; 6,410,248; 6,140,466; 6,200,759; and 6,242,568; as well as International Patent Publication Nos. WO 98/37186; WO 98/53057; WO 00/27878; and WO 01/88197 and GB 2,338,237. In addition, enhancement of binding specificity for zinc finger proteins has been described, for example, in International Patent Publication No. WO 02/077227.

In addition, as disclosed in these and other references, zinc finger domains and/or multi-fingered zinc finger proteins may be linked together using any suitable linker sequences, including for example, linkers of 5 or more amino acids in length. See, also, U.S. Pat. Nos. 6,479,626; 6,903,185; and 7,153,949 for exemplary linker sequences 6 or more amino acids in length. The proteins described herein may include any combination of suitable linkers between the individual zinc fingers of the protein. In addition, enhancement of binding specificity for zinc finger binding domains has been described, for example, in co-owned International Patent Publication No. WO 02/077227.

Zn finger proteins and methods for design and construction of fusion proteins (and polynucleotides encoding same) are known to those of skill in the art and described in detail in U.S. Pat. Nos. 6,140,081; 5,789,538; 6,453,242; 6,534,261; 5,925,523; 6,007,988; 6,013,453; and 6,200,759; International Patent Publication Nos. WO 95/19431; WO 96/06166; WO 98/53057; WO 98/54311; WO 00/27878; WO 01/60970; WO 01/88197; WO 02/099084; WO 98/53058; WO 98/53059; WO 98/53060; WO 02/016536; and WO 03/016496.

In addition, as disclosed in these and other references, Zn finger proteins and/or multi-fingered Zn finger proteins may be linked together, e.g., as a fusion protein, using any suitable linker sequences, including for example, linkers of 5 or more amino acids in length. See, also, U.S. Pat. Nos. 6,479,626; 6,903,185; and 7,153,949 for exemplary linker sequences 6 or more amino acids in length. The Zn finger molecules described herein may include any combination of suitable linkers between the individual zinc finger proteins and/or multi-fingered Zn finger proteins of the Zn finger molecule.

In certain embodiments, the DNA-binding domain or endonuclease domain comprises a Zn finger molecule comprising an engineered zinc finger protein that binds (in a sequence-specific manner) to a target DNA sequence. In some embodiments, the Zn finger molecule comprises one Zn finger protein or fragment thereof. In other embodiments, the Zn finger molecule comprises a plurality of Zn finger proteins (or fragments thereof), e.g., 2, 3, 4, 5, 6 or more Zn finger proteins (and optionally no more than 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, or 2 Zn finger proteins). In some embodiments, the Zn finger molecule comprises at least three Zn finger proteins. In some embodiments, the Zn finger molecule comprises four, five or six fingers. In some embodiments, the Zn finger molecule comprises 8, 9, 10, 11 or 12 fingers. In some embodiments, a Zn finger molecule comprising three Zn finger proteins recognizes a target DNA sequence comprising 9 or 10 nucleotides. In some embodiments, a Zn finger molecule comprising four Zn finger proteins recognizes a target DNA sequence comprising 12 to 14 nucleotides. In some embodiments, a Zn finger molecule comprising six Zn finger proteins recognizes a target DNA sequence comprising 18 to 21 nucleotides.

In some embodiments, a Zn finger molecule comprises a two-handed Zn finger protein. Two handed zinc finger proteins are those proteins in which two clusters of zinc finger proteins are separated by intervening amino acids so that the two zinc finger domains bind to two discontinuous target DNA sequences. An example of a two handed type of zinc finger binding protein is SIP1, where a cluster of four zinc finger proteins is located at the amino terminus of the protein and a cluster of three Zn finger proteins is located at the carboxyl terminus (see Remade, et al. (1999) EMBO Journal 18(18):5073-5084). Each cluster of zinc fingers in these proteins is able to bind to a unique target sequence and the spacing between the two target sequences can comprise many nucleotides

Linkers

In some embodiments, a gene modifying polypeptide may comprise a linker, e.g., a peptide linker, e.g., a linker as described in Table 1 or Table 10. In some embodiments, a gene modifying polypeptide comprises, in an N-terminal to C-terminal direction, a Cas domain (e.g., a Cas domain of Table 8), a linker of Table 10 (or a sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto), and an RT domain (e.g., an RT domain of Table 6). In some embodiments, a gene modifying polypeptide comprises a flexible linker between the endonuclease and the RT domain, e.g., a linker comprising the amino acid sequence SGGSSGGSSGSETPGTSESATPESSGGSSGGSS (SEQ ID NO: 11,002). In some embodiments, an RT domain of a gene modifying polypeptide may be located C-terminal to the endonuclease domain. In some embodiments, an RT domain of agene modifying polypeptide may be located N-terminal to the endonuclease domain. In some embodiments, a gene modifying polypeptide comprises an amino acid sequence as listed in Table A1, or a sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto.

TABLE 10 Exemplary linker sequences SEQ ID Amino Acid Sequence NO GGS GGSGGS 5102 GGSGGSGGS 5103 GGSGGSGGSGGS 5104 GGSGGSGGSGGSGGS 5105 GGSGGSGGSGGSGGSGGS 5106 GGGGS 5107 GGGGSGGGGS 5108 GGGGSGGGGSGGGGS 5109 GGGGSGGGGSGGGGSGGGGS 5110 GGGGSGGGGSGGGGSGGGGSGGGGS 5111 GGGGSGGGGSGGGGSGGGGSGGGGSGGGGS 5112 GGG GGGG 5114 GGGGG 5115 GGGGGG 5116 GGGGGGG 5117 GGGGGGGG 5118 GSS GSSGSS 5120 GSSGSSGSS 5121 GSSGSSGSSGSS 5122 GSSGSSGSSGSSGSS 5123 GSSGSSGSSGSSGSSGSS 5124 EAAAK 5125 EAAAKEAAAK 5126 EAAAKEAAAKEAAAK 5127 EAAAKEAAAKEAAAKEAAAK 5128 EAAAKEAAAKEAAAKEAAAKEAAAK 5129 EAAAKEAAAKEAAAKEAAAKEAAAKEAAAK 5130 PAP PAPAP 5132 PAPAPAP 5133 PAPAPAPAP 5134 PAPAPAPAPAP 5135 PAPAPAPAPAPAP 5136 GGSGGG 5137 GGGGGS 5138 GGSGSS 5139 GSSGGS 5140 GGSEAAAK 5141 EAAAKGGS 5142 GGSPAP 5143 PAPGGS 5144 GGGGSS 5145 GSSGGG 5146 GGGEAAAK 5147 EAAAKGGG 5148 GGGPAP 5149 PAPGGG 5150 GSSEAAAK 5151 EAAAKGSS 5152 GSSPAP 5153 PAPGSS 5154 EAAAKPAP 5155 PAPEAAAK 5156 GGSGGGGSS 5157 GGSGSSGGG 5158 GGGGGSGSS 5159 GGGGSSGGS 5160 GSSGGSGGG 5161 GSSGGGGGS 5162 GGSGGGEAAAK 5163 GGSEAAAKGGG 5164 GGGGGSEAAAK 5165 GGGEAAAKGGS 5166 EAAAKGGSGGG 5167 EAAAKGGGGGS 5168 GGSGGGPAP 5169 GGSPAPGGG 5170 GGGGGSPAP 5171 GGGPAPGGS 5172 PAPGGSGGG 5173 PAPGGGGGS 5174 GGSGSSEAAAK 5175 GGSEAAAKGSS 5176 GSSGGSEAAAK 5177 GSSEAAAKGGS 5178 EAAAKGGSGSS 5179 EAAAKGSSGGS 5180 GGSGSSPAP 5181 GGSPAPGSS 5182 GSSGGSPAP 5183 GSSPAPGGS 5184 PAPGGSGSS 5185 PAPGSSGGS 5186 GGSEAAAKPAP 5187 GGSPAPEAAAK 5188 EAAAKGGSPAP 5189 EAAAKPAPGGS 5190 PAPGGSEAAAK 5191 PAPEAAAKGGS 5192 GGGGSSEAAAK 5193 GGGEAAAKGSS 5194 GSSGGGEAAAK 5195 GSSEAAAKGGG 5196 EAAAKGGGGSS 5197 EAAAKGSSGGG 5198 GGGGSSPAP 5199 GGGPAPGSS 5200 GSSGGGPAP 5201 GSSPAPGGG 5202 PAPGGGGSS 5203 PAPGSSGGG 5204 GGGEAAAKPAP 5205 GGGPAPEAAAK 5206 EAAAKGGGPAP 5207 EAAAKPAPGGG 5208 PAPGGGEAAAK 5209 PAPEAAAKGGG 5210 GSSEAAAKPAP 5211 GSSPAPEAAAK 5212 EAAAKGSSPAP 5213 EAAAKPAPGSS 5214 PAPGSSEAAAK 5215 PAPEAAAKGSS 5216 AEAAAKEAAAKEAAAKEAAAKAL 5217 EAEAAAKEAAAKEAAAKEAAAKA GGGGSEAAAKGGGGS 5218 EAAAKGGGGSEAAAK 5219 SGSETPGTSESATPES 5220 GSAGSAAGSGEF 5221 SGGSSGGSSGSETPGTSESATPESSGGSSGGSS 5222

In some embodiments, a linker of a gene modifying polypeptide comprises a motif chosen from: (SGGS)_(n) (SEQ ID NO: 5025), (GGGS)_(n) (SEQ ID NO: 5026), (GGGGS)_(n) (SEQ ID NO: 5027), (G)_(n), (EAAAK)_(n) (SEQ ID NO: 5028), (GGS)_(n), or (XP)_(n).

Gene Modifying Polypeptide Selection by Pooled Screening

Candidate gene modifying polypeptides may be screened to evaluate a candidate's gene editing ability. For example, an RNA gene modifying system designed for the targeted editing of a coding sequence in the human genome may be used. In certain embodiments, such a gene modifying system may be used in conjunction with a pooled screening approach.

For example, a library of gene modifying polypeptide candidates and a template guide RNA (tgRNA) may be introduced into mammalian cells to test the candidates' gene editing abilities by a pooled screening approach. In specific embodiments, a library of gene modifying polypeptide candidates is introduced into mammalian cells followed by introduction of the tgRNA into the cells.

Representative, non-limiting examples of mammalian cells that may be used in screening include HEK293T cells, U2OS cells, HeLa cells, HepG2 cells, Huh7 cells, K562 cells, or iPS cells.

A gene modifying polypeptide candidate may comprise 1) a Cas-nuclease, for example a wild-type Cas nuclease, e.g., a wild-type Cas9 nuclease, a mutant Cas nuclease, e.g., a Cas nickase, for example, a Cas9 nickase such as a Cas9 N863A nickase, or a Cas nuclease selected from Table 7 or 8, 2) a peptide linker, e.g., a sequence from Table 1 or 10, that may exhibit varying degrees of length, flexibility, hydrophobicity, and/or secondary structure; and 3) a reverse transcriptase (RT), e.g. an RT domain from Table 1 or 6. A gene modifying polypeptide candidate library comprises: a plurality of different gene modifying polypeptide candidates that differ from each other with respect to one, two or all three of the Cas nuclease, peptide linker or RT domain components, or a plurality of nucleic acid expression vectors that encode such gene modifying polypeptide candidates.

For screening of gene modifying polypeptide candidates, a two-component system may be used that comprises a gene modifying polypeptide component and a tgRNA component. A gene modifying component may comprise, for example, an expression vector, e.g., an expression plasmid or lentiviral vector, that encodes a gene modifying polypeptide candidate, for example, comprises a human codon-optimized nucleic acid that encodes a gene modifying polypeptide candidate, e.g., a Cas-linker-RT fusion as described above. In a particular embodiment, a lentiviral cassette is utilized that comprises: (i) a promoter for expression in mammalian cells, e.g., a CMV promoter; (ii) a gene modifying library candidate, e.g. a Cas-linker-RT fusion comprising a Cas nuclease of Table 7 or 8, a peptide linker of Table 10 and an RT of Table 6, for example a Cas-linker-RT fusion as in Table 1; (iii) a self-cleaving polypeptide, e.g., a T2A peptide; (iv) a marker enabling selection in mammalian cells, e.g., a puromycin resistance gene; and (v) a termination signal, e.g., a poly A tail.

The tgRNA component may comprise a tgRNA or expression vector, e.g., an expression plasmid, that produces the tgRNA, for example, utilizes a U6 promoter to drive expression of the tgRNA, wherein the tgRNA is a non-coding RNA sequence that is recognized by Cas and localizes it to the genomic locus of interest, and that also templates reverse transcription of the desired edit into the genome by the RT domain.

To prepare a pool of cells expressing gene modifying polypeptide library candidates, mammalian cells, e.g., HEK293T or U2OS cells, may be transduced with pooled gene modifying polypeptide candidate expression vector preparations, e.g., lentiviral preparations, of the gene modifying candidate polypeptide library. In a particular embodiment, lentiviral plasmids are utilized, and HEK293 Lenti-X cells are seeded in 15 cm plates (˜12×10⁶ cells) prior to lentiviral plasmid transfection. In such an embodiment, lentiviral plasmid transfection may be performed using the Lentiviral Packaging Mix (Biosettia) and transfection of the plasmid DNA for the gene modifying candidate library is performed the following day using Lipofectamine 2000 and Opti-MEM media according to the manufacturer's protocol. In such an embodiment, extracellular DNA may be removed by a full media change the next day and virus-containing media may be harvested 48 hours after. Lentiviral media may be concentrated using Lenti-X Concentrator (TaKaRa Biosciences) and 5 mL lentiviral aliquots may be made and stored at −80° C. Lentiviral titering is performed by enumerating colony forming units post-selection, e.g., post Puromycin selection.

For monitoring gene editing of a target DNA, mammalian cells, e.g., HEK293T or U2OS cells, carrying a target DNA may be utilized. In other embodiments for monitoring gene editing of a target DNA, mammalian cells, e.g., HEK293T or U2OS cells, carrying a target DNA genomic landing pad may be utilized. In particular embodiments, the target DNA genomic landing pad may comprise a gene to be edited for treatment of a disease or disorder of interest. In other particular embodiments, the target DNA is a gene sequence that expresses a protein that exhibits detectable characteristics that may be monitored to determine whether gene editing has occurred. For example, in certain embodiments, a blue fluorescence protein (BFP)− or green fluorescence protein (GFP)-expressing genomic landing pad is utilized. In certain embodiments, mammalian cells, e.g., HEK293T or U2OS cells, comprising a target DNA, e.g., a target DNA genomic landing pad, are seeded in culture plates at 500×-3000× cells per gene modifying library candidate and transduced at a 0.2-0.3 multiplicity of infection (MOI) to minimize multiple infections per cell. Puromycin (2.5 ug/mL) may be added 48 hours post infection to allow for selection of infected cells. In such an embodiment, cells may be kept under puromycin selection for at least 7 days and then scaled up for tgRNA introduction, e.g., tgRNA electroporation.

To ascertain whether gene editing occurs, mammalian cells containing a target DNA to be edited may be infected with gene modifying polypeptide library candidates then transfected with tgRNA designed for use in editing of the target DNA. Subsequently, the cells may be analyzed to determine whether editing of the target locus has occurred according to the designed outcome, or whether no editing or imperfect editing has occurred, e.g., by using cell sorting and sequence analysis.

In a particular embodiment, to ascertain whether genome editing occurs, BFP- or GFP-expressing mammalian cells, e.g., HEK293T or U2OS cells, may be infected with gene modifying library candidates and then transfected or electroporated with tgRNA plasmid or RNA, e.g., by electroporation of 250,000 cells/well with 200 ng of a tgRNA plasmid designed to convert BFP-to-GFP or GFP-to-BFP, at a cell count ensuring >250×-1000× coverage per library candidate. In such an embodiment, the genome-editing capacity of the various constructs in this assay may be assessed by sorting the cells by Fluorescence-Activated Cell Sorting (FACS) for expression of the color-converted fluorescent protein (FP) at 4-10 days post-electroporation. Cells are sorted and harvested as distinct populations of unedited cells (exhibiting original florescence protein signal), edited cells (exhibiting converted fluorescence protein signal), and imperfect edit (exhibiting no florescence protein signal) cells. A sample of unsorted cells may also be harvested as the input population to determine candidate enrichment during analysis.

To determine which gene modifying library candidates exhibit genome-editing capacity in an assay, genomic DNA (gDNA) is harvested from the sorted cell populations, and analyzed by sequencing the gene modifying library candidates in each population. Briefly, gene modifying candidates may be amplified from the genome using primers specific to the gene modifying polypeptide expression vector, e.g., the lentiviral cassette, amplified in a second round of PCR to dilute genomic DNA, and then sequenced, for example, sequenced by a next-generation sequencing platform. After quality control of sequencing reads, reads of at least about 1500 nucleotides and generally no more than about 3200 nucleotides are mapped to the gene modifying polypeptide library sequences and those containing a minimum of about an 80% match to a library sequence are considered to be successfully aligned to a given candidate for purposes of this pooled screen. In order to identify candidates capable of performing gene editing in the assay, e.g., the BFP-to-GFP or GFP-to-BFP edit, the read count of each library candidate in the edited population is compared to its read count in the initial, unsorted population.

For purposes of pooled screening, gene modifying candidates with genome-editing capacity are identified based on enrichment in the edited (converted FP) population relative to unsorted (input) cells. In some embodiments, an enrichment of at least 1.0, 1.5, 2.0, 2.5, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0, 10, 15, 20, 25, 30, 40, 50, 60, 70, 80, 90, or at least 100-fold over the input indicates potentially useful gene editing activity, e.g., at least 2-fold enrichment. In some embodiments, the enrichment is converted to a log-value by taking the log base 2 of the enrichment ratio. In some embodiments, a log 2 enrichment score of at least 0, 1, 2, 3, 4, 5, 5.5, 6.0, 6.2, 6.3, 6.4, 6.5, or at least 6.6 indicates potentially useful gene editing activity, e.g., a log 2 enrichment score of at least 1.0. In particular embodiments, enrichment values observed for gene modifying candidates may be compared to enrichment values observed under similar conditions utilizing a reference, e.g., Element ID No: 17380 as listed in Example 7.

In some embodiments, multiple tgRNAs may be used to screen the gene modifying candidate library. In particular embodiments, a plurality of tgRNAs may be utilized to optimize template/Cas-linker-RT fusion pairs, e.g., for gene editing of particular target genes, for example, gene targets for the treatment of disease. In specific embodiments, a pooled approach to screening gene modifying candidates may be performed using a multiplicity of different tgRNAs in an arrayed format.

In some embodiments, multiple types of edits, e.g., insertions, substitutions, and/or deletions of different lengths, may be used to screen the gene modifying candidate library.

In some embodiments, multiple target sequences, e.g., different fluorescent proteins, may be used to screen the gene modifying candidate library. In some embodiments, multiple target sequences, e.g., different fluorescent proteins, may be used to screen the gene modifying candidate library. In some embodiments, multiple cell types, e.g., HEK293T or U2OS, may be used to screen the gene modifying candidate library. The person of ordinary skill in the art will appreciate that a given candidate may exhibit altered editing capacity or even the gain or loss of any observable or useful activity across different conditions, including tgRNA sequence (e.g., nucleotide modifications, PBS length, RT template length), target sequence, target location, type of edit, location of mutation relative to the first-strand nick of the gene modifying polypeptide, or cell type. Thus, in some embodiments, gene modifying library candidates are screened across multiple parameters, e.g., with at least two distinct tgRNAs in at least two cell types, and gene editing activity is identified by enrichment in any single condition. In other embodiments, a candidate with more robust activity across different tgRNA and cell types is identified by enrichment in at least two conditions, e.g., in all conditions screened. For clarity, candidates found to exhibit little to no enrichment under any given condition are not assumed to be inactive across all conditions and may be screened with different parameters or reconfigured at the polypeptide level, e.g., by swapping, shuffling, or evolving domains (e.g., RT domain), linkers, or other signals (e.g., NLS).

Sequences of Exemplary Cas9-Linker-RT Fusions

In some embodiments, a gene modifying polypeptide comprises a linker sequence and an RT sequence. In some embodiments, a gene modifying polypeptide comprises a linker sequence as listed in Table 1, or an amino acid sequence having at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto. In some embodiments, a gene modifying polypeptide comprises the amino acid sequence of an RT domain as listed in Table 1, or an amino acid sequence having at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto. In some embodiments, a gene modifying polypeptide comprises a linker sequence as listed in Table 1, or an amino acid sequence having at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto; and the amino acid sequence of an RT domain as listed in Table 1, or an amino acid sequence having at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto. In some embodiments, a gene modifying polypeptide comprises: (i) a linker sequence as listed in a row of Table 1, or an amino acid sequence having at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto; and (ii) the amino acid sequence of an RT domain as listed in the same row of Table 1, or an amino acid sequence having at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto.

Exemplary Gene Modifying Polypeptides

In some embodiments, a gene modifying polypeptide (e.g., a gene modifying polypeptide that is part of a system described herein) comprises an amino acid sequence of any one of SEQ ID NOs: 1-7743, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In some embodiments, a gene modifying polypeptide comprises an amino acid sequence of any one of SEQ ID NOs: 1-7743, or an amino acid sequence having at least 80% identity thereto. In some embodiments, a gene modifying polypeptide comprises an amino acid sequence of any one of SEQ ID NOs: 1-7743, or an amino acid sequence having at least 90% identity thereto. In some embodiments, a gene modifying polypeptide comprises an amino acid sequence of any one of SEQ ID NOs: 1-7743, or an amino acid sequence having at least 95% identity thereto. In some embodiments, a gene modifying polypeptide comprises an amino acid sequence of any one of SEQ ID NOs: 1-7743, or an amino acid sequence having at least 99% identity thereto. In some embodiments, a gene modifying polypeptide comprises an amino acid sequence of any one of SEQ ID NOs: 1-7743. In some embodiments, a gene modifying polypeptide comprises an amino acid sequence of any one of SEQ ID NOs: 6001-7743, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In some embodiments, a gene modifying polypeptide comprises an amino acid sequence of any one of SEQ ID NOs: 4501-4541, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto.

In some embodiments, a gene modifying polypeptide comprises an amino acid sequence as listed in Table A1, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto.

In some embodiments, a gene modifying polypeptide comprises an amino acid sequence of a SEQ ID NO as listed in Table D1, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In some embodiments, a gene modifying polypeptide comprises an amino acid sequence of a SEQ ID NO as listed in Table D2, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In some embodiments, a gene modifying polypeptide comprises an amino acid sequence of a SEQ ID NO as listed in Table D3, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In some embodiments, a gene modifying polypeptide comprises an amino acid sequence of a SEQ ID NO as listed in Table D4, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In some embodiments, a gene modifying polypeptide comprises an amino acid sequence of a SEQ ID NO as listed in Table D5, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In some embodiments, a gene modifying polypeptide comprises an amino acid sequence of a SEQ ID NO as listed in Table D6, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In some embodiments, a gene modifying polypeptide comprises an amino acid sequence of a SEQ ID NO as listed in Table D7, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In some embodiments, a gene modifying polypeptide comprises an amino acid sequence of a SEQ ID NO as listed in Table D8, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In some embodiments, a gene modifying polypeptide comprises an amino acid sequence of a SEQ ID NO as listed in Table D9, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In some embodiments, a gene modifying polypeptide comprises an amino acid sequence of a SEQ ID NO as listed in Table D10, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In some embodiments, a gene modifying polypeptide comprises an amino acid sequence of a SEQ ID NO as listed in Table D11, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In some embodiments, a gene modifying polypeptide comprises an amino acid sequence of a SEQ ID NO as listed in Table D12, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto.

In some embodiments, a gene modifying polypeptide comprises an amino acid sequence as listed in Table T1, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In some embodiments, a gene modifying polypeptide comprises a linker comprising a linker sequence as listed in Table T1, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In some embodiments, a gene modifying polypeptide comprises an RT domain comprising an RT domain sequence as listed in Table T1, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In some embodiments, a gene modifying polypeptide comprises: (i) a linker comprising a linker sequence as listed in a row of Table T1, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto; and (ii) an RT domain comprising an RT domain sequence as listed in the same row of Table T1, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto.

TABLE T1 Selection of exemplary gene modifying polypeptides SEQ ID NO: SEQ for Full ID Poly- NO: peptide of Sequence Linker Sequence linker RT name 1372 AEAAAKEAAAKEAAAK 15,401 AVIRE_P03360_ EAAAKALEAEAAAKE 3mutA AAAKEAAAKEAAAKA 1197 AEAAAKEAAAKEAAAK 15,402 FLV_P10273_ EAAAKALEAEAAAKE 3mutA AAAKEAAAKEAAAKA 2784 AEAAAKEAAAKEAAAK 15,403 MLVMS_P03355_ EAAAKALEAEAAAKE 3mutA_ AAAKEAAAKEAAAKA WS 647 AEAAAKEAAAKEAAAK 15,404 SFV3L_P27401_ EAAAKALEAEAAAKE 2mutA AAAKEAAAKEAAAKA

In some embodiments, a gene modifying polypeptide comprises an amino acid sequence as listed in Table T2, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In some embodiments, a gene modifying polypeptide comprises a linker comprising a linker sequence as listed in Table T2, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In some embodiments, a gene modifying polypeptide comprises an RT domain comprising an RT domain sequence as listed in Table T2, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In some embodiments, a gene modifying polypeptide comprises: (i) a linker comprising a linker sequence as listed in a row of Table T2, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto; and (ii) an RT domain comprising an RT domain sequence as listed in the same row of Table T2, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto.

TABLE T2 Selection of exemplary gene modifying polypeptides SEQ ID NO: SEQ for Full ID Poly- NO: peptide of Sequence Linker Sequence linker RT name 2311 GGGGSGGGGSGGGGSGGGGS 15,405 MLVCB_P08361_3mutA 1373 GGGGSGGGGSGGGGSGGGGSGGGGSGGGGS 15,406 AVIRE_P03360_3mutA 2644 GGGGSGGGGSGGGGSGGGGSGGGGGGGGS 15,407 MLVMS_P03355_PLV919 2304 GSSGSSGSSGSSGSSGSS 15,408 MLVCB_P08361_3mutA 2325 EAAAKEAAAKEAAAKEAAAK 15,409 MLVCB_P08361_3mutA 2322 EAAAKEAAAKEAAAKEAAAKEAAAKEAAAK 15,410 MLVCB_P08361_3mutA 2187 PAPAPAPAPAP 15,411 MLVBM_Q7SVK7_3mut 2309 PAPAPAPAPAPAP 15,412 MLVCB_P08361_3mutA 2534 PAPAPAPAPAPAP 15,413 MLVFF_P26809_3mutA 2797 PAPAPAPAPAPAP 15,414 MLVMS_P03355_3mutA WS 3084 PAPAPAPAPAPAP 15,415 MLVMS_P03355_3mutA_ WS 2868 PAPAPAPAPAPAP 15,416 MLVMS_P03355_PLV919 126 EAAAKGGG 15,417 PERV_Q4VFZ2_3mut 306 EAAAKGGG 15,418 PERV_Q4VFZ2_3mut 1410 PAPGGG 15,419 AVIRE_P03360_3mutA 804 GGGGSSGGS 15,420 WMSV_P03359_3mut 1937 GGGGGSEAAAK 15,421 BAEVM_P10272_3mutA 2721 GGGEAAAKGGS 15,422 MLVMS_P03355_3mut 3018 GGGEAAAKGGS 15,423 MLVMS_P03355_3mut 1018 GGGEAAAKGGS 15,424 XMRV6_A1Z651_3mutA 2317 GGSGGGPAP 15,425 MLVCB_P08361_3mutA 2649 PAPGGSGGG 15,426 MLVMS_P03355_PLV919 2878 PAPGGSGGG 15,427 MLVMS_P03355_PLV919 912 GGSEAAAKPAP 15,428 WMSV_P03359_3mutA 2338 GGSPAPEAAAK 15,429 MLVCB_P08361_3mutA 2527 GGSPAPEAAAK 15,430 MLVFF_P26809_3mutA 141 EAAAKGGSPAP 15,431 PERV_Q4VFZ2_3mut 341 EAAAKGGSPAP 15,432 PERV_Q4VFZ2_3mut 2315 EAAAKPAPGGS 15,433 MLVCB_P08361_3mutA 3080 EAAAKPAPGGS 15,434 MLVMS_P03355_3mutA_ WS 2688 GGGGSSEAAAK 15,435 MLVMS_P03355_PLV919 2885 GGGGSSEAAAK 15,436 MLVMS_P03355_PLV919 2810 GSSGGGEAAAK 15,437 MLVMS_P03355_3mutA_ WS 3057 GSSGGGEAAAK 15,438 MLVMS_P03355_3mutA_ WS 1861 GSSEAAAKGGG 15,439 MLVAV_P03356_3mutA 3056 GSSGGGPAP 15,440 MLVMS_P03355_3mutA_ WS 1038 GSSPAPGGG 15,441 XMRV6_A1Z651_3mutA 2308 PAPGGGGSS 15,442 MLVCB_P08361_3mutA 1672 GGGEAAAKPAP 15,443 KORV_Q9TTC1- Pro_3mutA 2526 GGGEAAAKPAP 15,444 MLVFF_P26809_3mutA 1938 GGGPAPEAAAK 15,445 BAEVM_P10272_3mutA 2641 GSSEAAAKPAP 15,446 MLVMS_P03355_PLV919 2891 GSSEAAAKPAP 15,447 MLVMS_P03355_PLV919 1225 GSSPAPEAAAK 15,448 FLV_P10273_3mutA 2839 GSSPAPEAAAK 15,449 MLVMS_P03355_3mutA_ WS 3127 GSSPAPEAAAK 15,450 MLVMS_P03355_3mutA_ WS 2798 PAPGSSEAAAK 15,451 MLVMS_P03355_3mutA_ WS 3091 PAPGSSEAAAK 15,452 MLVMS_P03355_3mutA_ WS 1372 AEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAA 15,453 AVIRE_P03360_3mutA AKEAAAKEAAAKA 1197 AEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAA 15,454 FLV_P10273_3mutA AKEAAAKEAAAKA 2611 AEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAA 15,455 MLVMS_P03355_PLV919 AKEAAAKEAAAKA 2784 AEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAA 15,456 MLVMS_P03355_3mutA_ AKEAAAKEAAAKA WS 480 AEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAA 15,457 SFV1_P23074_2mutA AKEAAAKEAAAKA 647 AEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAA 15,458 SFV3L_P27401_2mutA AKEAAAKEAAAKA 1006 AEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAA 15,459 XMRV6_A1Z651_3mutA AKEAAAKEAAAKA 2518 SGSETPGTSESATPES 15,460 MLVFF_P26809_3mutA

Subsequences of Exemplary Gene Modifying Polypeptides

In some embodiments, the gene modifying polypeptide comprises, in N-terminal to C-terminal order, one or more (e.g., 1, 2, 3, 4, 5, or all 6) of an N-terminal methionine residue, a first nuclear localization signal (NLS), a DNA binding domain, a linker, an RT domain, and/or a second NLS. In some embodiments, a gene modifying polypeptide comprises, in N-terminal to C-terminal order, a NLS (e.g., a first NLS), a DNA binding domain, a linker, and an RT domain, wherein the linker and RT domain are the linker and RT domain of a gene modifying polypeptide of any one of SEQ ID NOs: 1-7743, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity to said linker and RT domain. In some embodiments, a gene modifying polypeptide comprises, in N-terminal to C-terminal order, a DNA binding domain, a linker, an RT domain, and an NLS (e.g., a second NLS) wherein the linker and RT domain are the linker and RT domain of a gene modifying polypeptide of any one of SEQ ID NOs: 1-7743, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity to said linker and RT domain. In some embodiments, a gene modifying polypeptide comprises, in N-terminal to C-terminal order, a first NLS, a DNA binding domain, a linker, an RT domain, and a second NLS, wherein the linker and RT domain are the linker and RT domain of a gene modifying polypeptide of any one of SEQ ID NOs: 1-7743, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity to said linker and RT domain. In some embodiments, the gene modifying polypeptide further comprises an N-terminal methionine residue.

In some embodiments, the gene modifying polypeptide comprises, in N-terminal to C-terminal order, one or more (e.g., 1, 2, 3, 4, 5, or all 6) of an N-terminal methionine residue, a first nuclear localization signal (NLS) (e.g., of a gene modifying polypeptide of any one of SEQ ID NOs: 1-7743 and/or as listed in any of Tables A1, T1, T2, or D1-D12, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto), a DNA binding domain (e.g., a Cas domain, e.g., a SpyCas9 domain, e.g., as listed in Table 8, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto; or a DNA binding domain of a gene modifying polypeptide of any one of SEQ ID NOs: 1-7743 and/or as listed in any of Tables A1, T1, T2, or D1-D12, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto), a linker (e.g., of a gene modifying polypeptide of any one of SEQ ID NOs: 1-7743 and/or as listed in any of Tables A1, T1, T2, or D1-D12, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto), an RT domain (e.g., of a gene modifying polypeptide of any one of SEQ ID NOs: 1-7743 and/or as listed in any of Tables A1, T1, T2, or D1-D12, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto), and a second NLS (e.g., of a gene modifying polypeptide of any one of SEQ ID NOs: 1-7743 and/or as listed in any of Tables A1, T1, T2, or D1-D12, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto). In some embodiments, the gene modifying polypeptide further comprises (e.g., C-terminal to the second NLS) a T2A sequence and/or a puromycin sequence (e.g., of a gene modifying polypeptide of any one of SEQ ID NOs: 1-7743 and/or as listed in any of Tables A1, T1, T2, or D1-D12, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto). In some embodiments, a nucleic acid encoding a gene modifying polypeptide (e.g., as described herein) encodes a T2A sequence, e.g., wherein the T2A sequence is situated between a region encoding the gene modifying polypeptide and a second region, wherein the second region optionally encodes a selectable marker, e.g., puromycin.

In certain embodiments, the first NLS comprises a first NLS sequence of a gene modifying polypeptide having an amino acid sequence of any one of SEQ ID NOs: 1-7743, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In certain embodiments, the first NLS comprises a first NLS sequence of a gene modifying polypeptide as listed in any of Tables A1, T1, T2, or D1-D12, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In certain embodiments, the first NLS sequence comprises a C-myc NLS. In certain embodiments, the first NLS comprises the amino acid sequence PAAKRVKLD (SEQ ID NO: 11,095), or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto.

In certain embodiments, the gene modifying polypeptide further comprises a spacer sequence between the first NLS and the DNA binding domain. In certain embodiments, the spacer sequence between the first NLS and the DNA binding domain comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acids. In certain embodiments, the spacer sequence between the first NLS and the DNA binding domain comprises the amino acid sequence GG.

In certain embodiments, the DNA binding domain comprises a DNA binding domain of a gene modifying polypeptide of any one of SEQ ID NOs: 1-7743, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In certain embodiments, the DNA binding domain comprises a DNA binding domain of a gene modifying polypeptide as listed in any of Tables A1, T1, T2, or D1-D12, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In certain embodiments, the DNA binding domain comprises a Cas domain (e.g., as listed in Table 8). In certain embodiments, the DNA binding domain comprises the amino acid sequence of a SpyCas9 polypeptide (e.g., as listed in Table 8, e.g., a Cas9 N863A polypeptide), or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In certain embodiments, the DNA binding domain comprises the amino acid sequence:

(SEQ ID NO: 11,096) DKKYSIGLDIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHS IKKNLIGALLFDSGETAEATRLKRTARRRYTRRKNRICYL QEIFSNEMAKVDDSFFHRLEESFLVEEDKKHERHPIFGNI VDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLALAHMI KFRGHFLIEGDLNPDNSDVDKLFIQLVQTYNQLFEENPIN ASGVDAKAILSARLSKSRRLENLIAQLPGEKKNGLFGNLI ALSLGLTPNFKSNFDLAEDAKLQLSKDTYDDDLDNLLAQI GDQYADLFLAAKNLSDAILLSDILRVNTEITKAPLSASMI KRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSKNGYAGY IDGGASQEEFYKFIKPILEKMDGTEELLVKLNREDLLRKO RTFDNGSIPHQIHLGELHAILRRQEDFYPFLKDNREKIEK ILTFRIPYYVGPLARGNSRFAWMTRKSEETITPWNFEEVV DKGASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYFTVYN ELTKVKYVTEGMRKPAFLSGEQKKAIVDLLFKTNRKVTVK QLKEDYFKKIECFDSVEISGVEDRFNASLGTYHDLLKIIK DKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYAHL FDDKVMKQLKRRRYTGWGRLSRKLINGIRDKQSGKTILDF LKSDGFANRNFMQLIHDDSLTFKEDIQKAQVSGQGDSLHE HIANLAGSPAIKKGILQTVKVVDELVKVMGRHKPENIVIE MARENQTTQKGQKNSRERMKRIEEGIKELGSQILKEHPVE NTQLQNEKLYLYYLONGRDMYVDQELDINRLSDYDVDHIV PQSFLKDDSIDNKVLTRSDKARGKSDNVPSEEVVKKMKNY WRQLLNAKLITQRKFDNLTKAERGGLSELDKAGFIKRQLV ETRQITKHVAQILDSRMNTKYDENDKLIREVKVITLKSKL VSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYP KLESEFVYGDYKVYDVRKMIAKSEQEIGKATAKYFFYSNI MNFFKTEITLANGEIRKRPLIETNGETGEIVWDKGRDFAT VRKVLSMPQVNIVKKTEVQTGGFSKESILPKRNSDKLIAR KKDWDPKKYGGFDSPTVAYSVLVVAKVEKGKSKKLKSVKE LLGITIMERSSFEKNPIDFLEAKGYKEVKKDLIIKLPKYS LFELENGRKRMLASAGELQKGNELALPSKYVNFLYLASHY EKLKGSPEDNEQKOLFVEQHKHYLDEIIEQISEFSKRVIL ADANLDKVLSAYNKHRDKPIREQAENIIHLFTLTNLGAPA AFKYFDTTIDRKRYTSTKEVLDATLIHQSITGLYETRIDL SQLGGD, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto.

In certain embodiments, the gene modifying polypeptide further comprises a spacer sequence between the DNA binding domain and the linker. In certain embodiments, the spacer sequence between the DNA binding domain and the linker comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acids. In certain embodiments, the spacer sequence between the DNA binding domain and the linker comprises the amino acid sequence GG.

In certain embodiments, the linker comprises a linker sequence of a gene modifying polypeptide of any one of SEQ ID NOs: 1-7743, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In certain embodiments, the linker comprises a linker sequence of a gene modifying polypeptide as listed in any of Tables A1, T1, T2, or D1-D12, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In certain embodiments, the linker comprises an amino acid sequence as listed in Table 1 or 10, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto.

In certain embodiments, the gene modifying polypeptide further comprises a spacer sequence between the linker and the RT domain. In certain embodiments, the spacer sequence between the linker and the RT domain comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acids. In certain embodiments, the spacer sequence between the linker and the RT domain comprises the amino acid sequence GG.

In certain embodiments, the RT domain comprises a RT domain sequence of a gene modifying polypeptide of any one of SEQ ID NOs: 1-7743, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In certain embodiments, the RT domain comprises a RT domain sequence of a gene modifying polypeptide as listed in any of Tables A1, T1, T2, or D1-D12, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In certain embodiments, the RT domain comprises an amino acid sequence as listed in Table 1 or 6, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In some embodiments, the RT domain has a length of about 400-500, 500-600, 600-700, 700-800, 800-900, or 900-1000 amino acids.

In certain embodiments, the gene modifying polypeptide further comprises a spacer sequence between the RT domain and the second NLS. In certain embodiments, the spacer sequence between the RT domain and the second NLS comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acids. In certain embodiments, the spacer sequence between the RT domain and the second NLS comprises the amino acid sequence AG.

In certain embodiments, the second NLS comprises a second NLS sequence of a gene modifying polypeptide of any one of SEQ ID NOs: 1-7743. In certain embodiments, the second NLS comprises a second NLS sequence of a gene modifying polypeptide as listed in any of Tables A1, T1, T2, or D1-D12. In certain embodiments, the second NLS sequence comprises a plurality of partial NLS sequences. In embodiments, the NLS sequence, e.g., the second NLS sequence, comprises a first partial NLS sequence, e.g., comprising the amino acid sequence KRTADGSEFE (SEQ ID NO: 11,097), or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In embodiments, the NLS sequence, e.g., the second NLS sequence, comprises a second partial NLS sequence. In embodiments, the NLS sequence, e.g., the second NLS sequence, comprises an SV40A5 NLS, e.g., a bipartite SV40A5 NLS, e.g., comprising the amino acid sequence KRTADGSEFESPKKKAKVE (SEQ ID NO: 11,098), or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In certain embodiments, the NLS sequence, e.g., the second NLS sequence, comprises the amino acid sequence KRTADGSEFEKRTADGSEFESPKKKAKVE (SEQ ID NO: 11,099), or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto.

In certain embodiments, the gene modifying polypeptide further comprises a spacer sequence between the second NLS and the T2A sequence and/or puromycin sequence. In certain embodiments, the spacer sequence between the second NLS and the T2A sequence and/or puromycin sequence comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acids. In certain embodiments, the spacer sequence between the second NLS and the T2A sequence and/or puromycin sequence comprises the amino acid sequence GSG.

Linkers and RT Domains

In some embodiments, the gene modifying polypeptide comprises a linker (e.g., as described herein) and an RT domain (e.g., as described herein). In certain embodiments, the gene modifying polypeptide comprises, in N-terminal to C-terminal order, a linker (e.g., as described herein) and an RT domain (e.g., as described herein).

In certain embodiments, the linker comprises a linker sequence as listed in Table 10, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In certain embodiments, the linker comprises a linker sequence of any one of SEQ ID NOs: 1-7743, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In certain embodiments, the linker comprises a linker sequence of any one of SEQ ID NOs: 6001-7743, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In certain embodiments, the linker comprises a linker sequence of any one of SEQ ID NOs: 4501-4541, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In certain embodiments, the linker comprises a linker sequence of an exemplary gene modifying polypeptide listed in Table A1, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In certain embodiments, the linker comprises a linker sequence of a gene modifying polypeptide having the amino acid sequence of a SEQ ID NO: listed in Table T1, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In certain embodiments, the linker comprises a linker sequence of a gene modifying polypeptide having the amino acid sequence of a SEQ ID NO: listed in Table T2, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In certain embodiments, the linker comprises a linker sequence of a gene modifying polypeptide having the amino acid sequence of a SEQ ID NO: listed in Table D1, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In certain embodiments, the linker comprises a linker sequence of a gene modifying polypeptide having the amino acid sequence of a SEQ ID NO: listed in Table D2, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In certain embodiments, the linker comprises a linker sequence of a gene modifying polypeptide having the amino acid sequence of a SEQ ID NO: listed in Table D3, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In certain embodiments, the linker comprises a linker sequence of a gene modifying polypeptide having the amino acid sequence of a SEQ ID NO: listed in Table D4, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In certain embodiments, the linker comprises a linker sequence of a gene modifying polypeptide having the amino acid sequence of a SEQ ID NO: listed in Table D5, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In certain embodiments, the linker comprises a linker sequence of a gene modifying polypeptide having the amino acid sequence of a SEQ ID NO: listed in Table D6, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In certain embodiments, the linker comprises a linker sequence of a gene modifying polypeptide having the amino acid sequence of a SEQ ID NO: listed in Table D7, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In certain embodiments, the linker comprises a linker sequence of a gene modifying polypeptide having the amino acid sequence of a SEQ ID NO: listed in Table D8, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In certain embodiments, the linker comprises a linker sequence of a gene modifying polypeptide having the amino acid sequence of a SEQ ID NO: listed in Table D9, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In certain embodiments, the linker comprises a linker sequence of a gene modifying polypeptide having the amino acid sequence of a SEQ ID NO: listed in Table D10, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In certain embodiments, the linker comprises a linker sequence of a gene modifying polypeptide having the amino acid sequence of a SEQ ID NO: listed in Table D11, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In certain embodiments, the linker comprises a linker sequence of a gene modifying polypeptide having the amino acid sequence of a SEQ ID NO: listed in Table D12, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto.

In certain embodiments, the RT domain comprises an RT domain sequence as listed in Table 6, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In certain embodiments, the RT domain comprises an RT domain sequence of an exemplary gene modifying polypeptide listed in Table A1, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In certain embodiments, the RT domain comprises a RT domain sequence of a gene modifying polypeptide having the amino acid sequence of a SEQ ID NO: listed in Table T1, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In certain embodiments, the RT domain comprises a RT domain sequence of a gene modifying polypeptide having the amino acid sequence of a SEQ ID NO: listed in Table T2, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In certain embodiments, the RT domain comprises a RT domain sequence of a gene modifying polypeptide having the amino acid sequence of a SEQ ID NO: listed in Table D1, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In certain embodiments, the RT domain comprises a RT domain sequence of a gene modifying polypeptide having the amino acid sequence of a SEQ ID NO: listed in Table D2, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In certain embodiments, the RT domain comprises a RT domain sequence of a gene modifying polypeptide having the amino acid sequence of a SEQ ID NO: listed in Table D3, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In certain embodiments, the RT domain comprises a RT domain sequence of a gene modifying polypeptide having the amino acid sequence of a SEQ ID NO: listed in Table D4, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In certain embodiments, the RT domain comprises a RT domain sequence of a gene modifying polypeptide having the amino acid sequence of a SEQ ID NO: listed in Table D5, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In certain embodiments, the RT domain comprises a RT domain sequence of a gene modifying polypeptide having the amino acid sequence of a SEQ ID NO: listed in Table D6, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In certain embodiments, the RT domain comprises a RT domain sequence of a gene modifying polypeptide having the amino acid sequence of a SEQ ID NO: listed in Table D7, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In certain embodiments, the RT domain comprises a RT domain sequence of a gene modifying polypeptide having the amino acid sequence of a SEQ ID NO: listed in Table D8, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In certain embodiments, the RT domain comprises a RT domain sequence of a gene modifying polypeptide having the amino acid sequence of a SEQ ID NO: listed in Table D9, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In certain embodiments, the RT domain comprises a RT domain sequence of a gene modifying polypeptide having the amino acid sequence of a SEQ ID NO: listed in Table D10, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In certain embodiments, the RT domain comprises a RT domain sequence of a gene modifying polypeptide having the amino acid sequence of a SEQ ID NO: listed in Table D11, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In certain embodiments, the RT domain comprises a RT domain sequence of a gene modifying polypeptide having the amino acid sequence of a SEQ ID NO: listed in Table D12, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto.

In some embodiments, a gene modifying polypeptide comprises a portion of a gene modifying polypeptide of any one of SEQ ID NOs: 1-7743, wherein the portion comprises a linker and RT domain, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity to said portion.

In some embodiments, a gene modifying polypeptide comprises a linker of a gene modifying polypeptide of any one of SEQ ID NOs: 1-7743, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity to said linker. In some embodiments, a gene modifying polypeptide comprises a linker of a gene modifying polypeptide of any one of SEQ ID NOs: 6001-7743, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity to said linker. In some embodiments, a gene modifying polypeptide comprises a linker of a gene modifying polypeptide of any one of SEQ ID NOs: 4501-4541, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity to said linker. In some embodiments, a gene modifying polypeptide comprises a linker of a gene modifying polypeptide as listed in any of Tables A1, T1, T2, or D1-D12, or a linker comprising an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto.

In some embodiments, a gene modifying polypeptide comprises an RT domain of a gene modifying polypeptide of any one of SEQ ID NOs: 1-7743, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity to said RT domain. In some embodiments, a gene modifying polypeptide comprises an RT domain of a gene modifying polypeptide of any one of SEQ ID NOs: 6001-7743, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity said RT domain. In some embodiments, a gene modifying polypeptide comprises an RT domain of a gene modifying polypeptide of any one of SEQ ID NOs: 4501-4541, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity said RT domain. In some embodiments, a gene modifying polypeptide comprises an RT domain of a gene modifying polypeptide as listed in any of Tables A1, T1, T2, or D1-D12, or an RT domain comprising an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto.

In certain embodiments, the linker and the RT domain of a gene modifying polypeptide comprise the amino acid sequences of a linker and RT domain (or amino acid sequences having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto) of a gene modifying polypeptide having the amino acid sequence of any one of SEQ ID NOs: 1-7743. In certain embodiments, the linker and the RT domain of a gene modifying polypeptide comprise amino acid sequences of a linker and RT domain having at least 80% identity to the linker and RT domains of any one of SEQ ID NOs: 1-7743. In certain embodiments, the linker and the RT domain of a gene modifying polypeptide comprise amino acid sequences of a linker and RT domain having at least 90% identity to the linker and RT domains of any one of SEQ ID NOs: 1-7743. In certain embodiments, the linker and the RT domain of a gene modifying polypeptide comprise amino acid sequences of a linker and RT domain having at least 95% identity to the linker and RT domains of any one of SEQ ID NOs: 1-7743. In certain embodiments, the linker and the RT domain of a gene modifying polypeptide comprise amino acid sequences of a linker and RT domain having at least 99% identity to the linker and RT domains of any one of SEQ ID NOs: 1-7743. In certain embodiments, the linker and the RT domain of a gene modifying polypeptide comprise the amino acid sequences of a linker and RT domain (or amino acid sequences having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto) of a gene modifying polypeptide having the amino acid sequence of any one of SEQ ID NOs: 6001-7743. In certain embodiments, the linker and the RT domain of a gene modifying polypeptide comprise the amino acid sequences of a linker and RT domain (or amino acid sequences having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto) of a gene modifying polypeptide having the amino acid sequence of any one of SEQ ID NOs: 4501-4541. In certain embodiments, the linker and the RT domain of a gene modifying polypeptide comprise the amino acid sequences of a linker and RT domain (or amino acid sequences having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto) from a single row of any of Tables A1, T1, T2, or D1-D12 (e.g., from a single exemplary gene modifying polypeptide as listed in any of Tables A1, T1, T2, or D1-D12).

In certain embodiments, the linker and the RT domain of a gene modifying polypeptide comprise the amino acid sequences of a linker and RT domain (or amino acid sequences having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto) from two different amino acid sequences selected from SEQ ID NOs: 1-7743. In certain embodiments, the linker and the RT domain of a gene modifying polypeptide comprise the amino acid sequences of a linker and RT domain (or amino acid sequences having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto) from different rows of any of Tables A1, T1, T2, or D1-D12.

In certain embodiments, the gene modifying polypeptide further comprises a first NLS (e.g., a 5′ NLS), e.g., as described herein. In certain embodiments, the gene modifying polypeptide further comprises a second NLS (e.g., a 3′ NLS), e.g., as described herein. In certain embodiments, the gene modifying polypeptide further comprises an N-terminal methionine residue.

RT Families and Mutants

In certain embodiments, a gene modifying polypeptide comprises the amino acid sequence of an RT domain sequence from a family selected from: AVIRE, BAEVM, FFV, FLV, FOAMV, GALV, KORV, MLVAV, MLVBM, MLVCB, MLVFF, MLVMS, PERV, SFV1, SFV3L, WMSV, XMRV6, BLVAU, BLVJ, HTL1A, HTL1C, HTL1L, HTL32, HTL3P, HTLV2, JSRV, MLVF5, MLVRD, MMTVB, MPMV, SFVCP, SMRVH, SRV1, SRV2, and WDSV. In certain embodiments, a gene modifying polypeptide comprises the amino acid sequence of an RT domain sequence from a family selected from: AVIRE, BAEVM, FFV, FLV, FOAMV, GALV, KORV, MLVAV, MLVBM, MLVCB, MLVFF, MLVMS, PERV, SFV1, SFV3L, WMSV, and XMRV6.

In certain embodiments, a gene modifying polypeptide comprises the amino acid sequence of an RT domain sequence from an MLVMS RT domain. In embodiments, the amino acid sequence of an RT domain sequence comprises one or more point mutations as listed in column 1 of Table M1, or a point mutation corresponding thereto. In embodiments, the amino acid sequence of an RT domain sequence comprises one or more point mutations as listed in column 3 of Table M1 (MLVMS), or a point mutation corresponding thereto. In embodiments, the amino acid sequence of an RT domain sequence comprises one or more point mutations at an amino acid position of the RT domain as listed in columns 1 and 2 of Table M2, or an amino acid position corresponding thereto.

In certain embodiments, a gene modifying polypeptide comprises the amino acid sequence of an RT domain sequence from an AVIRE RT domain. In embodiments, the amino acid sequence of an RT domain sequence comprises one or more point mutations as listed in column 2 of Table M1, or a point mutation corresponding thereto. In embodiments, the amino acid sequence of an RT domain sequence comprises one or more point mutations as listed in column 4 of Table M1 (AVIRE), or a point mutation corresponding thereto. In embodiments, the amino acid sequence of an RT domain sequence comprises one or more point mutations at an amino acid position of the RT domain as listed in columns 3 and 4 of Table M2, or an amino acid position corresponding thereto. In certain embodiments, the RT domain comprises an IENSSP (SEQ ID NO: 15465) (e.g., at the C-terminus).

TABLE M1 Exemplary point mutations in MLVMS and AVIRE RT domains RT-linker filing Corresponding MLVMS AVIRE (MLVMS) AVIRE (PLV4921) (PLV10990) H8Y P51L Q51L S67R T67R E67K E67K E69K E69K T197A T197A D200N D200N D200N D200N H204R N204R E302K E302K T306K T306K F309N Y309N W313F W313F W313F W313F T330P G330P T330P G330P L435G T436G N454K N455K D524G D526G E562Q E564Q D583N D585N H594Q H596Q L603W L605W L603W L605W D653N D655N L671P L673P IENSSP (SEQ ID NO: 15465) at C- term

TABLE M2 Positions that can be mutated in exemplary MLVMS and AVIRE RT domains WT residue & position MLVMS position # AVIRE MLVMS aa * AVIRE aa position # H 8 Y 8 P 51 Q 51 S 67 T 67 E 69 E 69 T 197 T 197 D 200 D 200 H 204 N 204 E 302 E 302 T 306 T 306 F 309 Y 309 W 313 W 313 T 330 G 330 L 435 T 436 N 454 N 455 D 524 D 526 E 562 E 564 D 583 D 585 H 594 H 596 L 603 L 605 D 653 D 655 L 671 S 673

In certain embodiments, a gene modifying polypeptide comprises a gamma retrovirus derived RT domain. In certain embodiments, the gamma retrovirus-derived RT domain of a gene modifying polypeptide comprises the amino acid sequence of an RT domain sequence from a family selected from: AVIRE, BAEVM, FFV, FLV, FOAMV, GALV, KORV, MLVAV, MLVBM, MLVCB, MLVFF, MLVMS, PERV, SFV1, SFV3L, WMSV, and XMRV6. In some embodiments, the gamma retrovirus-derived RT domain of a gene modifying polypeptide is not derived from PERV. In some embodiments, said RT includes one, two, three, four, five, six or more mutations shown in Table 2 and corresponding to mutations D200N, L603W, T330P, D524G, E562Q, D583N, P51L, S67R, E67K, T197A, H204R, E302K, F309N, W313F, L435G, N454K, H594Q, L671P, E69K, or D653N in the RT domain of murine leukemia virus reverse transcriptase. In some embodiments, the gene modifying polypeptide further comprises a linker having at least 99% identity to a linker domains of any one of SEQ ID NOs: 1-7743. In some embodiments, the gene modifying polypeptide further comprises a linker having at least 99% or 100% identity to SEQ ID NO: 5217 or SEQ ID NO:11,041.

In embodiments, the RT domain comprises the amino acid sequence of an RT domain of an AVIRE RT (e.g., an AVIRE_P03360 sequence, e.g., SEQ ID NO: 8001), or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In some embodiments, the RT domain comprises the amino acid sequence of an AVIRE RT further comprising one, two, three, four, or five mutations selected from the group consisting of D200N, G330P, L605W, T306K, and W313F, or a corresponding position in a homologous RT domain. In some embodiments, the RT domain comprises the amino acid sequence of an AVIRE RT further comprising one, two, or three mutations selected from the group consisting of D200N, G330P, and L605W, or a corresponding position in a homologous RT domain.

In embodiments, the RT domain comprises the amino acid sequence of an RT domain of a BAEVM RT (e.g., an BAEVM_P10272 sequence, e.g., SEQ ID NO: 8004), or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In some embodiments, the RT domain comprises the amino acid sequence of a BAEVM RT further comprising one, two, three, four, or five mutations selected from the group consisting of D198N, E328P, L602W, T304K, and W311F, or a corresponding position in a homologous RT domain. In some embodiments, the RT domain comprises the amino acid sequence of a BAEVM RT further comprising one, two, or three mutations selected from the group consisting of D198N, E328P, and L602W, or a corresponding position in a homologous RT domain.

In embodiments, the RT domain comprises the amino acid sequence of an RT domain of an FFV RT (e.g., an FFV_O93209 sequence, e.g., SEQ ID NO: 8012), or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In some embodiments, the RT domain comprises the amino acid sequence of an FFV RT further comprising one, two, three, or four mutations selected from the group consisting of D21N, T293N, T419P, and L393K, or a corresponding position in a homologous RT domain. In some embodiments, the RT domain comprises the amino acid sequence of an FFV RT further comprising one, two, or three mutations selected from the group consisting of D21N, T293N, and T419P, or a corresponding position in a homologous RT domain. In some embodiments, the RT domain comprises the amino acid sequence of an FFV RT further comprising the mutation D21N. In some embodiments, the RT domain comprises the amino acid sequence of an FFV RT further comprising one, two, or three mutations selected from the group consisting of T207N, T333P, and L307K, or a corresponding position in a homologous RT domain. In some embodiments, the RT domain comprises the amino acid sequence of an FFV RT further comprising one or two mutations selected from the group consisting of T207N and T333P, or a corresponding position in a homologous RT domain.

In embodiments, the RT domain comprises the amino acid sequence of an RT domain of an FLV RT (e.g., an FLV_P10273 sequence, e.g., SEQ ID NO: 8019), or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In some embodiments, the RT domain comprises the amino acid sequence of an FLV RT further comprising one, two, three, or four mutations selected from the group consisting of D199N, L602W, T305K, and W312F, or a corresponding position in a homologous RT domain. In some embodiments, the RT domain comprises the amino acid sequence of an FLV RT further comprising one or two mutations selected from the group consisting of D199N and L602W, or a corresponding position in a homologous RT domain.

In embodiments, the RT domain comprises the amino acid sequence of an RT domain of a FOAMV RT (e.g., an FOAMV_P14350 sequence, e.g., SEQ ID NO: 8021), or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In some embodiments, the RT domain comprises the amino acid sequence of an FOAMV RT further comprising one, two, three, or four mutations selected from the group consisting of D24N, T296N, S420P, and L396K, or a corresponding position in a homologous RT domain. In some embodiments, the RT domain comprises the amino acid sequence of an FOAMV RT further comprising one, two, or three mutations selected from the group consisting of D24N, T296N, and S420P, or a corresponding position in a homologous RT domain. In some embodiments, the RT domain comprises the amino acid sequence of an FOAMV RT further comprising the mutation D24N, or a corresponding position in a homologous RT domain. In some embodiments, the RT domain comprises the amino acid sequence of an FOAMV RT further comprising one, two, or three mutations selected from the group consisting of T207N, S331P, and L307K, or a corresponding position in a homologous RT domain. In some embodiments, the RT domain comprises the amino acid sequence of an FOAMV RT further comprising one or two mutations selected from the group consisting of T207N and S331P, or a corresponding position in a homologous RT domain.

In embodiments, the RT domain comprises the amino acid sequence of an RT domain of a GALV RT (e.g., an GALV_P21414 sequence, e.g., SEQ ID NO: 8027), or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In some embodiments, the RT domain comprises the amino acid sequence of a GALV RT further comprising one, two, three, four, or five mutations selected from the group consisting of D198N, E328P, L600W, T304K, and W311F, or a corresponding position in a homologous RT domain. In some embodiments, the RT domain comprises the amino acid sequence of a GALV RT further comprising one, two, or three mutations selected from the group consisting of D198N, E328P, and L600W, or a corresponding position in a homologous RT domain.

In embodiments, the RT domain comprises the amino acid sequence of an RT domain of a KORV RT (e.g., an KORV_Q9TTC1 sequence, e.g., SEQ ID NO: 8047), or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In some embodiments, the RT domain comprises the amino acid sequence of a GALV RT further comprising one, two, three, four, five, or six mutations selected from the group consisting of D32N, D322N, E452P, L274W, T428K, and W435F, or a corresponding position in a homologous RT domain. In some embodiments, the RT domain comprises the amino acid sequence of a GALV RT further comprising one, two, three, or four mutations selected from the group consisting of D32N, D322N, E452P, and L274W, or a corresponding position in a homologous RT domain. In some embodiments, the RT domain comprises the amino acid sequence of a GALV RT further comprising the mutation D32N. In some embodiments, the RT domain comprises the amino acid sequence of a KORV RT further comprising one, two, three, four, or five mutations selected from the group consisting of D231N, E361P, L633W, T337K, and W344F, or a corresponding position in a homologous RT domain. In some embodiments, the RT domain comprises the amino acid sequence of a KORV RT further comprising one, two, or three mutations selected from the group consisting of D231N, E361P, and L633W, or a corresponding position in a homologous RT domain.

In embodiments, the RT domain comprises the amino acid sequence of an RT domain of a MLVAV RT (e.g., an MLVAV_P03356 sequence, e.g., SEQ ID NO: 8053), or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In some embodiments, the RT domain comprises the amino acid sequence of a MLVAV RT further comprising one, two, three, four, or five mutations selected from the group consisting of D200N, T330P, L603W, T306K, and W313F, or a corresponding position in a homologous RT domain. In some embodiments, the RT domain comprises the amino acid sequence of a MLVAV RT further comprising one, two, or three mutations selected from the group consisting of D200N, T330P, and L603W, or a corresponding position in a homologous RT domain.

In embodiments, the RT domain comprises the amino acid sequence of an RT domain of a MLVBM RT (e.g., an MLVBM_Q7SVK7 sequence, e.g., SEQ ID NO: 8056), or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In some embodiments, the RT domain comprises the amino acid sequence of a MLVBM RT further comprising one, two, three, four, or five mutations selected from the group consisting of D199N, T329P, L602W, T305K, and W312F, or a corresponding position in a homologous RT domain. In some embodiments, the RT domain comprises the amino acid sequence of a MLVBM RT further comprising one, two, and three mutations selected from the group consisting of D200N, T330P, and L603W, or a corresponding position in a homologous RT domain.

In embodiments, the RT domain comprises the amino acid sequence of an RT domain of a MLVCB RT (e.g., an MLVCB_P08361 sequence, e.g., SEQ ID NO: 8062), or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In some embodiments, the RT domain comprises the amino acid sequence of a MLVCB RT further comprising one, two, three, four, or five mutations selected from the group consisting of D200N, T330P, L603W, T306K, and W313F, or a corresponding position in a homologous RT domain. In some embodiments, the RT domain comprises the amino acid sequence of a MLVCB RT further comprising one, two, and three mutations selected from the group consisting of D200N, T330P, and L603W, or a corresponding position in a homologous RT domain.

In embodiments, the RT domain comprises the amino acid sequence of an RT domain of a MLVFF RT, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In some embodiments, the RT domain comprises the amino acid sequence of a MLVFF RT further comprising one, two, three, four, or five mutations selected from the group consisting of D200N, T330P, L603W, T306K, and W313F, or a corresponding position in a homologous RT domain. In some embodiments, the RT domain comprises the amino acid sequence of a MLVFF RT further comprising one, two, and three mutations selected from the group consisting of D200N, T330P, and L603W, or a corresponding position in a homologous RT domain.

In embodiments, the RT domain comprises the amino acid sequence of an RT domain of a MLVMS RT (e.g., an MLVMS_reference sequence, e.g., SEQ ID NO: 8137; or an MLVMS_P03355 sequence, e.g., SEQ ID NO: 8070), or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In some embodiments, the RT domain comprises the amino acid sequence of a MLVMS RT further comprising one, two, three, four, five, or six mutations selected from the group consisting of D200N, T330P, L603W, T306K, W313F, and H8Y, or a corresponding position in a homologous RT domain. In some embodiments, the RT domain comprises the amino acid sequence of a MLVMS RT further comprising one, two, three, four, or five mutations selected from the group consisting of D200N, T330P, L603W, T306K, and W313F, or a corresponding position in a homologous RT domain. In some embodiments, the RT domain comprises the amino acid sequence of a MLVMS RT further comprising one, two, or three mutations selected from the group consisting of D200N, T330P, and L603W, or a corresponding position in a homologous RT domain.

In embodiments, the RT domain comprises the amino acid sequence of an RT domain of a PERV RT (e.g., an PERV_Q4VFZ2 sequence, e.g., SEQ ID NO: 8099), or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In some embodiments, the RT domain comprises the amino acid sequence of a PERV RT further comprising one, two, three, four, or five mutations selected from the group consisting of D196N, E326P, L599W, T302K, and W309F, or a corresponding position in a homologous RT domain. In some embodiments, the RT domain comprises the amino acid sequence of a PERV RT further comprising one, two, or three mutations selected from the group consisting of D196N, E326P, and L599W, or a corresponding position in a homologous RT domain.

In embodiments, the RT domain comprises the amino acid sequence of an RT domain of a SFV1 RT (e.g., an SFV1_P23074 sequence, e.g., SEQ ID NO: 8105), or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In some embodiments, the RT domain comprises the amino acid sequence of a SFV1 RT further comprising one, two, three, or four mutations selected from the group consisting of D24N, T296N, N420P, and L396K, or a corresponding position in a homologous RT domain. In some embodiments, the RT domain comprises the amino acid sequence of a SFV1 RT further comprising one, two, or three mutations selected from the group consisting of D24N, T296N, and N420P, or a corresponding position in a homologous RT domain. In some embodiments, the RT domain comprises the amino acid sequence of a SFV1 RT further comprising the D24N, or a corresponding position in a homologous RT domain.

In embodiments, the RT domain comprises the amino acid sequence of an RT domain of a SFV3L RT (e.g., an SFV3L_P27401 sequence, e.g., SEQ ID NO: 8111), or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In some embodiments, the RT domain comprises the amino acid sequence of a SFV3L RT further comprising one, two, three, or four mutations selected from the group consisting of D24N, T296N, N422P, and L396K, or a corresponding position in a homologous RT domain. In some embodiments, the RT domain comprises the amino acid sequence of a SFV3L RT further comprising one, two, or three mutations selected from the group consisting of D24N, T296N, and N422P, or a corresponding position in a homologous RT domain. In some embodiments, the RT domain comprises the amino acid sequence of a SFV3L RT further comprising the mutation D24N, or a corresponding position in a homologous RT domain. In some embodiments, the RT domain comprises the amino acid sequence of a SFV3L RT further comprising one, two, or three mutations selected from the group consisting of T307N, N333P, and L307K, or a corresponding position in a homologous RT domain. In some embodiments, the RT domain comprises the amino acid sequence of a SFV3L RT further comprising one or two mutations selected from the group consisting of T307N and N333P, or a corresponding position in a homologous RT domain.

In embodiments, the RT domain comprises the amino acid sequence of an RT domain of a WMSV RT (e.g., an WMSV_P03359 sequence, e.g., SEQ ID NO: 8131), or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In some embodiments, the RT domain comprises the amino acid sequence of a WMSV RT further comprising one, two, three, four, or five mutations selected from the group consisting of D198N, E328P, L600W, T304K, and W311F, or a corresponding position in a homologous RT domain. In some embodiments, the RT domain comprises the amino acid sequence of a WMSV RT further comprising one, two, or three mutations selected from the group consisting of D198N, E328P, and L600W, or a corresponding position in a homologous RT domain.

In embodiments, the RT domain comprises the amino acid sequence of an RT domain of a XMRV6 RT (e.g., an XMRV6_A1Z651 sequence, e.g., SEQ ID NO: 8134), or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In some embodiments, the RT domain comprises the amino acid sequence of a XMRV6 RT further comprising one, two, three, four, or five mutations selected from the group consisting of D200N, T330P, L603W, T306K, and W313F, or a corresponding position in a homologous RT domain. In some embodiments, the RT domain comprises the amino acid sequence of a XMRV6 RT further comprising one, two, or three mutations selected from the group consisting of D200N, T330P, and L603W, or a corresponding position in a homologous RT domain.

In certain embodiments, the RT domain of a gene modifying polypeptide comprises the amino acid sequence of an RT domain of an AVIRE RT, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In embodiments, the RT domain comprises the amino acid sequence of an RT domain comprised in a sequence listed in column 1 of Table A5, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In some embodiments, the gene modifying polypeptide further comprises a linker having at least 99% or 100% identity to SEQ ID NO: 5217 or SEQ ID NO:11,041.

In certain embodiments, the RT domain of a gene modifying polypeptide comprises the amino acid sequence of an RT domain of an MLVMS RT, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In embodiments, the RT domain comprises the amino acid sequence of an RT domain comprised in a sequence listed in any of columns 2-6 of Table A5, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In some embodiments, the gene modifying polypeptide further comprises a linker having at least 99% or 100% identity to SEQ ID NO: 5217 or SEQ ID NO:11,041.

TABLE A5 Exemplary gene modifying polypeptides comprising an AVIRE RT domain or an MLVMS RT domain. AVIRE SEQ ID NOs: MLVMS SEQ ID NOs:   1 2704 3007 3038 2638 2930   2 2706 3007 3038 2639 2930   3 2708 3008 3039 2639 2931   4 2709 3008 3039 2640 2931   5 2709 3009 3040 2640 2932   6 2710 3010 3040 2641 2932   7 2957 3010 3041 2641 2933   9 2957 3011 3041 2642 2933  10 2958 3012 3042 2642 2934  12 2959 3012 3042 2643 2934  13 2960 3013 3043 2643 2935  14 2962 3013 3043 2644 2935 6076 6042 3014 3044 2644 2936 6143 6068 3014 3044 2645 2936 6200 6097 3015 3045 2645 2937 6254 6136 3015 3045 2646 2937 6274 6156 3016 3046 2646 2938 6315 6215 3016 3046 2647 2938 6328 6216 3017 3047 2647 2939 6337 6301 3018 3047 2648 2939 6403 6352 3018 3048 2648 2940 6420 6365 3019 3048 2649 2940 6440 6411 3019 3049 2649 2941 6513 6436 3020 3049 2650 2941 6552 6458 3020 3050 2650 2942 6613 6459 3021 3051 2651 2942 6671 6524 3021 3051 2651 2943 6822 6562 3022 3052 2652 2943 6840 6563 3023 3052 2652 2944 6884 6699 3023 3053 2653 2945 6907 6865 3024 3053 2653 2945 6970 7022 3024 3054 2654 2946 7025 7037 3025 3054 2655 2946 7052 7088 3025 3055 2655 2947 7078 7116 3026 3055 2656 2947 7243 7175 3026 3056 2656 2948 7253 7200 3027 3056 2657 2948 7318 7206 3027 3057 2657 2949 7379 7277 3028 3057 2658 2949 7486 7294 3028 3058 2658 2950 7524 7330 3029 3058 2659 2950 7668 7411 3030 3059 2659 2951 7680 7455 3030 3059 2660 2951 7720 7477 3031 3060 2660 2952 1137 7511 3031 3060 2661 2952 1138 7538 3032 3061 2661 2953 1139 7559 3032 3061 2662 2953 1140 7560 3033 3062 2662 2954 1141 7593 3033 3062 2663 2954 1142 7594 3034 3063 2663 2955 1143 7607 3034 3063 2664 2955 1144 7623 6025 3064 2664 6485 1145 7638 6041 3064 2665 6486 1146 7717 6043 3065 2665 6504 1147 7731 6098 3065 2666 6505 1148 7732 6099 3066 2666 6595 1149 2711 6180 3066 2667 6596 1150 2711 6182 3067 2667 6751 1151 2712 6237 3067 2668 6752 1152 2712 6238 3068 2668 6777 1153 2713 6311 3068 2669 6778 1154 2713 6312 3069 2669 7172 1155 2714 6578 3069 2670 7174 1156 2714 6579 3070 2670 7313 1157 2715 6663 3070 2671 7314 1158 2715 6664 3071 2671 1159 2716 6708 3071 2672 1160 2716 6709 3072 2672 1161 2717 6809 3072 2673 1162 2717 6831 3073 2673 1163 2718 6832 3073 2674 1164 2718 6864 3074 2674 1165 2719 6866 3074 2675 1166 2719 7089 3075 2675 1167 2720 7157 3075 2676 6015 2720 7159 3076 2676 6029 2721 7173 3076 2677 6045 2721 7176 3077 2677 6077 2722 7293 3077 2678 6129 2722 7295 3078 2678 6144 2723 7343 3078 2679 6164 2723 7393 3079 2680 6201 2724 7394 3079 2680 6227 2724 7425 3080 2681 6244 2725 7426 3080 2681 6250 2725 7444 3081 2682 6264 2726 7445 308: 2682 6289 2726 7476 3082 2683 6304 2727 7478 3082 2683 6316 2727 7496 3083 2684 6384 2728 7497 3083 2684 6421 2728 7537 3084 2685 6441 2729 7539 3084 2685 6492 2729 2780 3085 2686 6514 2730 2780 3085 2686 6530 2730 2781 3086 2687 6569 2731 2781 3086 2687 6584 2731 2782 3087 2688 6621 2732 2782 3087 2688 6651 2732 2783 3088 2689 6659 2733 2783 3088 2689 6683 2734 2784 3089 2690 6703 2734 2784 3089 2690 6727 2735 2785 3090 2691 6732 2735 2785 3090 2692 6745 2736 2786 3091 2692 6755 2736 2786 3091 2693 6784 2737 2787 3092 2693 6817 2737 2787 3092 2694 6823 2738 2788 3093 2694 6841 2739 2788 3093 2695 6871 2740 2789 3094 2695 6885 2740 2789 3095 2696 6898 2741 2790 3095 2696 6908 2741 2790 3096 2697 6933 2742 2791 3096 2697 6971 2742 2791 3097 2698 7009 2743 2792 3097 2698 7018 2743 2792 3098 2699 7045 2744 2793 3098 2699 7053 2744 2793 3099 2700 7068 2745 2794 3099 2700 7079 2745 2794 3100 2701 7096 2746 2795 3100 2701 7104 2746 2795 3101 2702 7122 2747 2796 3101 2702 7151 2747 2796 3102 2703 7163 2748 2797 3102 2703 7181 2748 2797 3103 2862 7244 2749 2798 3103 2862 7273 2750 2798 3104 2863 7319 2750 2799 3104 2863 7336 2751 2799 3105 2864 7380 2751 2800 3105 2864 7402 2752 2800 3106 2865 7462 2752 2801 3106 2865 7487 2753 2801 3107 2866 7525 2753 2802 3107 2866 7569 2754 2802 3108 2867 7626 2754 2803 3108 2867 7689 2755 2803 3109 2868 7707 2755 2804 3109 2868 7721 2756 2804 3110 2869 1371 2756 2805 3110 2869 1372 2757 2805 3111 2870 1373 2758 2806 3111 2870 1374 2758 2806 3112 2871 1375 2759 2807 3112 2871 1376 2759 2807 3113 2872 1377 2760 2808 3113 2872 1378 2760 2808 3114 2873 1379 2761 2809 3114 2873 1380 2761 2809 3115 2874 1381 2762 2810 3115 2874 1382 2762 2810 3116 2875 1383 2763 2811 3116 2875 1384 2763 2811 3117 2876 1385 2764 2812 3117 2876 1386 2764 2812 3118 2877 1387 2765 2813 3118 2877 1388 2765 2813 3119 2878 1389 2766 2814 3119 2878 1390 2766 2814 3120 2879 1391 2767 2815 3120 2879 1392 2767 2815 3121 2880 1393 2768 2816 3121 2880 1394 2768 2816 3122 2881 1395 2769 2817 3122 2881 1396 2769 2817 3123 2882 1397 2770 2818 3123 2882 1398 2770 2818 3124 2883 1399 2771 2819 3124 2883 1400 2771 2819 3125 2884 1401 2772 2820 3125 2884 1402 2773 2820 3126 2885 1403 2773 2821 3126 2885 1404 2774 2821 3127 2886 1405 2774 2822 3127 2886 1406 2775 2822 3128 2887 1407 2775 2823 3128 2887 1408 2776 2823 3129 2888 1409 2776 2824 3129 2888 1410 2777 2824 3130 2889 1411 2777 2825 3130 2889 1412 2778 2825 3131 2890 1413 2779 2826 3131 2890 1414 2779 2826 3132 2891 1415 2965 2827 3133 2891 1416 2965 2827 3133 2892 1417 2966 2828 3134 2893 1418 2966 2828 3134 2893 1419 2967 2829 3135 2894 1420 2968 2829 3135 2894 1421 2968 2830 3136 2895 1422 2969 2830 3136 2895 1423 2969 2831 6181 2896 1424 2970 2831 6183 2896 1425 2970 2832 6284 2897 1426 2971 2832 6285 2897 1427 2971 2833 6760 2898 1428 2972 2833 6761 2898 1429 2972 2834 7036 2899 1430 2973 2834 7038 2899 1431 2974 2835 7158 2900 1432 2974 2835 7160 2900 1433 2975 2836 2610 2901 1434 2976 2836 2610 2901 1435 2976 2837 2611 2902 1436 2977 2837 2611 2902 1437 2977 2838 2612 2903 1439 2978 2838 2612 2903 1440 2978 2839 2613 2904 1441 2979 2839 2613 2904 1442 2979 2840 2614 2905 1443 2980 2840 2614 2905 1444 2980 2841 2615 2906 1445 2981 2841 2615 2906 1446 2981 2842 2616 2907 1447 2982 2842 2616 2907 6001 2982 2843 2617 2908 6030 2983 2843 2617 2908 6078 2983 2844 2618 2909 6108 2984 2844 2618 2909 6130 2985 2845 2619 2910 6165 2985 2845 2619 2910 6265 2986 2846 2620 2911 6275 2987 2846 2620 2911 6305 2987 2847 2621 2912 6329 2988 2847 2621 2912 6370 2988 2848 2622 2913 6385 2989 2848 2622 2913 6404 2989 2849 2623 2914 6531 2990 2849 2623 2914 6585 2990 2850 2624 2915 6622 2991 2850 2624 2915 6652 2991 2851 2625 2916 6733 2992 2851 2625 2916 6756 2992 2852 2626 2917 6765 2993 2852 2626 2917 6798 2993 2853 2627 2918 6824 2994 2853 2627 2919 6972 2994 2854 2628 2919 7046 2995 2854 2628 2920 7054 2995 2855 2629 2920 7069 2996 2855 2629 2921 7080 2996 2856 2630 2921 7105 2997 2856 2630 2922 7123 2998 2857 2631 2922 7143 2998 2857 2631 2923 7152 2999 2858 2632 2923 7204 2999 2858 2632 2924 7320 3001 2859 2633 2924 7351 3001 2859 2633 2925 7381 3002 2860 2634 2925 7403 3002 2860 2634 2926 7438 3003 2861 2635 2926 7488 3003 2861 2635 2927 7500 3004 3035 2636 2927 7526 3004 3036 2636 2928 7588 3005 3036 2637 2928 7612 3005 3037 2637 2929 7627 3006 3037 2638 2929

Systems

In an aspect, the disclosure relates to a system comprising nucleic acid molecule encoding a gene modifying polypeptide (e.g., as described herein) and a template nucleic acid (e.g., a template RNA, e.g., as described herein). In certain embodiments, the nucleic acid molecule encoding the gene modifying polypeptide comprises one or more silent mutations in the coding region (e.g., in the sequence encoding the RT domain) relative to a nucleic acid molecule as described herein. In certain embodiments, the system further comprises a gRNA (e.g., a gRNA that binds to a polypeptide that induces a nick, e.g., in the opposite strand of the target DNA bound by the gene modifying polypeptide).

In certain embodiments, the nucleic acid molecule encoding the gene modifying polypeptide encodes a polypeptide having an amino acid sequence selected from SEQ ID NOs: 1-7743, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In certain embodiments, the nucleic acid molecule encoding the gene modifying polypeptide encodes a polypeptide having an amino acid sequence selected from SEQ ID NOs: 6001-7743, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In certain embodiments, the nucleic acid molecule encoding the gene modifying polypeptide encodes a polypeptide having an amino acid sequence selected from SEQ ID NOs: 4501-4541, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In certain embodiments, the nucleic acid molecule encoding the gene modifying polypeptide encodes a polypeptide as listed in any of Tables A1, T1, T2, or D1-D12, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto.

In certain embodiments, the nucleic acid molecule encoding the gene modifying polypeptide comprises a sequence encoding a portion of an amino acid sequence selected from SEQ ID NOs: 1-7743, wherein the portion comprises a linker and RT domain, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity to said portion. In certain embodiments, the nucleic acid molecule encoding the gene modifying polypeptide comprises a sequence encoding a portion of an amino acid sequence selected from SEQ ID NOs: 6001-7743, wherein the portion comprises a linker and RT domain, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity to said portion. In certain embodiments, the nucleic acid molecule encoding the gene modifying polypeptide comprises a sequence encoding a portion of an amino acid sequence selected from SEQ ID NOs: 4501-4541, wherein the portion comprises a linker and RT domain, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity to said portion. In certain embodiments, the nucleic acid molecule encoding the gene modifying polypeptide comprises a sequence encoding a portion of a polypeptide listed in any of Tables A1, T1, T2, or D1-D12, wherein the portion comprises a linker and RT domain, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity to said portion.

In certain embodiments, the nucleic acid molecule encoding the gene modifying polypeptide comprises a sequence encoding the linker of an amino acid sequence selected from SEQ ID NOs: 1-7743, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In certain embodiments, the nucleic acid molecule encoding the gene modifying polypeptide comprises a sequence encoding the linker of a polypeptide having an amino acid sequence selected from SEQ ID NOs: 6001-7743, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In certain embodiments, the nucleic acid molecule encoding the gene modifying polypeptide comprises a sequence encoding the linker of a polypeptide having an amino acid sequence selected from SEQ ID NOs: 4501-4541, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In certain embodiments, the nucleic acid molecule encoding the gene modifying polypeptide comprises a sequence encoding the linker of a polypeptide as listed in any of Tables A1, T1, T2, or D1-D12, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto.

In certain embodiments, the nucleic acid molecule encoding the gene modifying polypeptide comprises a sequence encoding the RT domain of an amino acid sequence selected from SEQ ID NOs: 1-7743, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In certain embodiments, the nucleic acid molecule encoding the gene modifying polypeptide comprises a sequence encoding the RT domain of a polypeptide having an amino acid sequence selected from SEQ ID NOs: 6001-7743, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In certain embodiments, the nucleic acid molecule encoding the gene modifying polypeptide comprises a sequence encoding the RT domain of a polypeptide having an amino acid sequence selected from SEQ ID NOs: 4501-4541, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In certain embodiments, the nucleic acid molecule encoding the gene modifying polypeptide comprises a sequence encoding the RT domain of a polypeptide as listed in any of Tables A1, T1, T2, or D1-D12, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto.

In an aspect, the disclosure relates to a system comprising a gene modifying polypeptide (e.g., as described herein) and a template nucleic acid (e.g., a template RNA, e.g., as described herein).

In certain embodiments, the gene modifying polypeptide comprises a polypeptide having an amino acid sequence selected from SEQ ID NOs: 1-7743, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In certain embodiments, the gene modifying polypeptide comprises a polypeptide having an amino acid sequence selected from SEQ ID NOs: 6001-7743, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In certain embodiments, the gene modifying polypeptide comprises a polypeptide having an amino acid sequence selected from SEQ ID NOs: 4501-4541, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In certain embodiments, the gene modifying polypeptide comprises a polypeptide as listed in any of Tables A1, T1, T2, or D1-D12, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto.

In certain embodiments, the gene modifying polypeptide comprises a portion of an amino acid sequence selected from SEQ ID NOs: 1-7743, wherein the portion comprises a linker and RT domain, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity to said portion. In certain embodiments, the gene modifying polypeptide comprises a portion of an amino acid sequence selected from SEQ ID NOs: 6001-7743, wherein the portion comprises a linker and RT domain, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity to said portion. In certain embodiments, the gene modifying polypeptide comprises a portion of an amino acid sequence selected from SEQ ID NOs: 4501-4541, wherein the portion comprises a linker and RT domain, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity to said portion. In certain embodiments, the gene modifying polypeptide comprises a portion of a polypeptide listed in any of Tables A1, T1, T2, or D1-D12, wherein the portion comprises a linker and RT domain, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity to said portion.

In certain embodiments, the gene modifying polypeptide comprises the linker of an amino acid sequence selected from SEQ ID NOs: 1-7743, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In certain embodiments, the gene modifying polypeptide comprises a sequence encoding the linker of a polypeptide having an amino acid sequence selected from SEQ ID NOs: 6001-7743, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In certain embodiments, the gene modifying polypeptide comprises a sequence encoding the linker of a polypeptide having an amino acid sequence selected from SEQ ID NOs: 4501-4541, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In certain embodiments, the gene modifying polypeptide comprises the linker of a polypeptide as listed in any of Tables A1, T1, T2, or D1-D12, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto.

In certain embodiments, the gene modifying polypeptide comprises the RT domain of an amino acid sequence selected from SEQ ID NOs: 1-7743, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In certain embodiments, the gene modifying polypeptide comprises a sequence encoding the RT domain of a polypeptide having an amino acid sequence selected from SEQ ID NOs: 6001-7743, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In certain embodiments, the gene modifying polypeptide comprises a sequence encoding the RT domain of a polypeptide having an amino acid sequence selected from SEQ ID NOs: 4501-4541, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto. In certain embodiments, the gene modifying polypeptide comprises the RT domain of a polypeptide as listed in any of Tables A1, T1, T2, or D1-D12, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity thereto.

Lengthy table referenced here US20240002886A1-20240104-T00001 Please refer to the end of the specification for access instructions.

Localization Sequences for Gene Modifying Systems

In certain embodiments, a gene editor system RNA further comprises an intracellular localization sequence, e.g., a nuclear localization sequence (NLS). In some embodiments, a gene modifying polypeptide comprises an NLS as comprised in SEQ ID NO: 4000 and/or SEQ ID NO: 4001, or an NLS having an amino acid sequence having at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto.

The nuclear localization sequence may be an RNA sequence that promotes the import of the RNA into the nucleus. In certain embodiments the nuclear localization signal is located on the template RNA. In certain embodiments, the gene modifying polypeptide is encoded on a first RNA, and the template RNA is a second, separate, RNA, and the nuclear localization signal is located on the template RNA and not on an RNA encoding the gene modifying polypeptide. While not wishing to be bound by theory, in some embodiments, the RNA encoding the gene modifying polypeptide is targeted primarily to the cytoplasm to promote its translation, while the template RNA is targeted primarily to the nucleus to promote insertion into the genome. In some embodiments the nuclear localization signal is at the 3′ end, 5′ end, or in an internal region of the template RNA. In some embodiments the nuclear localization signal is 3′ of the heterologous sequence (e.g., is directly 3′ of the heterologous sequence) or is 5′ of the heterologous sequence (e.g., is directly 5′ of the heterologous sequence). In some embodiments the nuclear localization signal is placed outside of the 5′ UTR or outside of the 3′ UTR of the template RNA. In some embodiments the nuclear localization signal is placed between the 5′ UTR and the 3′ UTR, wherein optionally the nuclear localization signal is not transcribed with the transgene (e.g., the nuclear localization signal is an anti-sense orientation or is downstream of a transcriptional termination signal or polyadenylation signal). In some embodiments the nuclear localization sequence is situated inside of an intron. In some embodiments a plurality of the same or different nuclear localization signals are in the RNA, e.g., in the template RNA. In some embodiments the nuclear localization signal is less than 5, 10, 25, 50, 75, 100, 150, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900 or 1000 bp in length. Various RNA nuclear localization sequences can be used. For example, Lubelsky and Ulitsky, Nature 555 (107-111), 2018 describe RNA sequences which drive RNA localization into the nucleus. In some embodiments, the nuclear localization signal is a SINE-derived nuclear RNA localization (SIRLOIN) signal. In some embodiments the nuclear localization signal binds a nuclear-enriched protein. In some embodiments the nuclear localization signal binds the HNRNPK protein. In some embodiments the nuclear localization signal is rich in pyrimidines, e.g., is a C/T rich, C/U rich, C rich, T rich, or U rich region. In some embodiments the nuclear localization signal is derived from a long non-coding RNA. In some embodiments the nuclear localization signal is derived from MALAT1 long non-coding RNA or is the 600 nucleotide M region of MALAT1 (described in Miyagawa et al., RNA 18, (738-751), 2012). In some embodiments the nuclear localization signal is derived from BORG long non-coding RNA or is a AGCCC motif (described in Zhang et al., Molecular and Cellular Biology 34, 2318-2329 (2014). In some embodiments the nuclear localization sequence is described in Shukla et al., The EMBO Journal e98452 (2018). In some embodiments the nuclear localization signal is derived from a retrovirus.

In some embodiments, a polypeptide described herein comprises one or more (e.g., 2, 3, 4, 5) nuclear targeting sequences, for example a nuclear localization sequence (NLS). In some embodiments, the NLS is a bipartite NLS. In some embodiments, an NLS facilitates the import of a protein comprising an NLS into the cell nucleus. In some embodiments, the NLS is fused to the N-terminus of a gene modifying polypeptide as described herein. In some embodiments, the NLS is fused to the C-terminus of the gene modifying polypeptide. In some embodiments, the NLS is fused to the N-terminus or the C-terminus of a Cas domain. In some embodiments, a linker sequence is disposed between the NLS and the neighboring domain of the gene modifying polypeptide.

In some embodiments, an NLS comprises the amino acid sequence MDSLLMNRRKFLYQFKNVRWAKGRRETYLC (SEQ ID NO: 5009), PKKRKVEGADKRTADGSEFESPKKKRKV(SEQ ID NO: 5010), RKSGKIAAIWKRPRKPKKKRKV (SEQ ID NO: 5011) KRTADGSEFESPKKKRKV(SEQ ID NO: 5012), KKTELQTTNAENKTKKL (SEQ ID NO: 5013), or KRGINDRNFWRGENGRKTR (SEQ ID NO: 5014), KRPAATKKAGQAKKKK (SEQ ID NO: 5015), PAAKRVKLD (SEQ ID NO: 4644), KRTADGSEFEKRTADGSEFESPKKKAKVE (SEQ ID NO: 4649), KRTADGSEFE (SEQ ID NO: 4650), KRTADGSEFESPKKKAKVE (SEQ ID NO: 4651), AGKRTADGSEFEKRTADGSEFESPKKKAKVE (SEQ ID NO: 4001) or a functional fragment or variant thereof. Exemplary NLS sequences are also described in PCT/EP2000/011690, the contents of which are incorporated herein by reference for their disclosure of exemplary nuclear localization sequences. In some embodiments, an NLS comprises an amino acid sequence as disclosed in Table 11. An NLS of this table may be utilized with one or more copies in a polypeptide in one or more locations in a polypeptide, e.g., 1, 2, 3 or more copies of an NLS in an N-terminal domain, between peptide domains, in a C-terminal domain, or in a combination of locations, in order to improve subcellular localization to the nucleus. Multiple unique sequences may be used within a single polypeptide. Sequences may be naturally monopartite or bipartite, e.g., having one or two stretches of basic amino acids, or may be used as chimeric bipartite sequences. Sequence references correspond to UniProt accession numbers, except where indicated as SeqNLS for sequences mined using a subcellular localization prediction algorithm (Lin et al BMC Bioinformat 13:157 (2012), incorporated herein by reference in its entirety).

TABLE 11 Exemplary nuclear localization signals for use in gene modifying systems Sequence Sequence References SEQ ID No. AHFKISGEKRPSTDPGKKAKNPKKKKKKDP Q76IQ7 5223 AHRAKKMSKTHA P21827 5224 ASPEYVNLPINGNG SeqNLS 5225 CTKRPRW 088622, Q86W56, Q9QYM2, O02776 5226 DKAKRVSRNKSEKKRR 015516, Q5RAK8, Q91YB2, Q91YB0, Q8QGQ6, 008785, Q9WVS9, 5227 Q6YGZ4 EELRLKEELLKGIYA Q9QY16, Q9UHLO, Q2TBP1, Q9QY15 5228 EEQLRRRKNSRLNNTG G5EFF5 5229 EVLKVIRTGKRKKKAWKRMVTKVC SeqNLS 5230 HHHHHHHHHHHHQPH Q63934, G3V7L5, Q12837 5231 HKKKHPDASVNFSEFSK P10103, Q4R844, P12682, B0CM99, A9RA84, Q6YKA4, P09429, 5232 P63159, Q08IE6, P63158, Q9YH06, B1MTB0 HKRTKK Q2R2D5 5233 IINGRKLKLKKSRRRSSQTSNNSFTSRRS SeqNLS 5234 KAEQERRK Q8LH59 5235 KEKRKRREELFIEQKKRK SeqNLS 5236 KKGKDEWFSRGKKP P30999 5237 KKGPSVQKRKKT Q6ZN17 5238 KKKTVINDLLHYKKEK SeqNLS, P32354 5239 KKNGGKGKNKPSAKIKK SeqNLS 5240 KKPKWDDFKKKKK Q15397, Q8BKS9, Q562C7 5241 KKRKKD SeqNLS, Q91Z62, Q1A730, Q969P5, Q2KHT6, Q9CPU7 5242 KKRRKRRRK SeqNLS 5243 KKRRRRARK Q9UMS6, D4A702, Q91YE8 5244 KKSKRGR Q9UBS0 5245 KKSRKRGS B4FG96 5246 KKSTALSRELGKIMRRR SeqNLS, P32354 5247 KKSYQDPEIIAHSRPRK Q9U7C9 5248 KKTGKNRKLKSKRVKTR Q9Z301, 054943, Q8K3T2 5249 KKVSIAGQSGKLWRWKR Q6YUL8 5250 KKYENVVIKRSPRKRGRPRK SeqNLS 5251 KNKKRK SeqNLS 5252 KPKKKR SeqNLS 5253 KRAMKDDSHGNSTSPKRRK Q0E671 5254 KRANSNLVAAYEKAKKK P23508 5255 KRASEDTTSGSPPKKSSAGPKR Q9BZZ5, Q5R644 5256 KRFKRRWMVRKMKTKK SeqNLS 5257 KRGLNSSFETSPKKVK Q8IV63 5258 KRGNSSIGPNDLSKRKQRKK SeqNLS 5259 KRIHSVSLSQSQIDPSKKVKRAK SeqNLS 5260 KRKGKLKNKGSKRKK 015381 5261 KRRRRRRREKRKR Q96GM8 5262 KRSNDRTYSPEEEKQRRA Q91ZF2 5263 KRTVATNGDASGAHRAKKMSK SeqNLS 5264 KRVYNKGEDEQEHLPKGKKR SeqNLS 5265 KSGKAPRRRAVSMDNSNK Q9WVH4, 043524 5266 KVNFLDMSLDDIIIYKELE Q9P127 5267 KVQHRIAKKTTRRRR Q9DXE6 5268 LSPSLSPL Q9Y261, P32182, P35583 5269 MDSLLMNRRKFLYQFKNVRWAKGRRETYLC Q9GZX7 5270 MPQNEYIELHRKRYGYRLDYHEKKRKKES SeqNLS 5271 REAHERSKKAKKMIGLKAKLYHK MVQLRPRASR SeqNLS 5272 NNKLLAKRRKGGASPKDDPMDDIK Q965G5 5273 NYKRPMDGTYGPPAKRHEGE 014497, A2BH40 5274 PDTKRAKLDSSETTMVKKK SeqNLS 5275 PEKRTKI SeqNLS 5276 PGGRGKKK Q719N1, Q9UBP0, A2VDN5 5277 PGKMDKGEHRQERRDRPY Q01844, Q61545 5278 PKKGDKYDKTD Q45FA5 5279 PKKKSRK 035914, Q01954 5280 PKKNKPE Q22663 5281 PKKRAKV P04295, P89438 5282 PKPKKLKVE P55263, P55262, P55264, Q64640 5283 PKRGRGR Q9FYS5, Q43386 5284 PKRRLVDDA POC797 5285 PKRRRTY SeqNLS 5286 PLFKRR A8X6H4, Q9TXJO 5287 PLRKAKR Q86WB0, Q5R8V9 5288 PPAKRKCIF Q6AZ28, 075928, Q8C5D8 5289 PPARRRRL Q8NAG6 5290 PPKKKRKV Q3L6L5, P03070, P14999, P03071 5291 PPNKRMKVKH Q8BN78 5292 PPRIYPQLPSAPT POC799 5293 PQRSPFPKSSVKR SeqNLS 5294 PRPRKVPR POC799 5295 PRRRVQRKR SeqNLS, Q5R448, Q5TAQ9 5296 PRRVRLK Q58DJ0, P56477, Q13568 5297 PSRKRPR Q62315, Q5F363, Q92833 5298 PSSKKRKV SeqNLS 5299 PTKKRVK P07664 5300 QRPGPYDRP SeqNLS 5301 RGKGGKGLGKGGAKRHRK SeqNLS 5302 RKAGKGGGGHKTTKKRSAKDEKVP B4FG96 5303 RKIKLKRAK A1L3G9 5304 RKIKRKRAK B9X187 5305 RKKEAPGPREELRSRGR 035126, P54258, Q5IS70, P54259 5306 RKKRKGK SeqNLS, Q29243, Q62165, Q28685, 018738, Q9TSZ6, Q14118 5307 RKKRRQRRR P04326, P69697, P69698, P05907, P20879, P04613, P19553, POC1J9, 5308 P20893, P12506, P04612, Q73370, POC1K0, P05906, P35965, P04609, P04610, P04614, P04608, P05905 RKKSIPLSIKNLKRKHKRKKNKITR Q9C0C9 5309 RKLVKPKNTKMKTKLRTNPY Q14190 5310 RKRLILSDKGQLDWKK SeqNLS, Q91Z62, Q1A730, Q2KHT6, Q9CPU7 5311 RKRLKSK Q13309 5312 RKRRVRDNM Q8QPH4, Q809M7, A8C8X1, Q2VNC5, Q38SQ0, 089749, Q6DNQ9, 5313 Q809L9, Q0A429, Q20NV3, P16509, P16505, Q6DNQ5, P16506, Q6XT06, P26118, Q2ICQ2, Q2RCG8, Q0A2DO, Q0A2H9, Q9IQ46, Q809M3, Q6J847, Q6J856, B4URE4, A4GCM7, Q0A440, P26120, P16511, RKRSPKDKKEKDLDGAGKRRKT Q7RTP6 5314 RKRTPRVDGQTGENDMNKRRRK 094851 5315 RLPVRRRRRR P04499, P12541, P03269, P48313, P03270 5316 RLRFRKPKSK P69469 5317 RQQRKR Q14980 5318 RRDLNSSFETSPKKVK Q8K3G5 5319 RRDRAKLR Q9SLB8 5320 RRGDGRRR Q80WE1, Q5R9B4, Q06787, P35922 5321 RRGRKRKAEKQ Q812D1, Q5XXA9, Q99JF8, Q8MJG1, Q66T72, 075475 5322 RRKKRR QOVD86, Q58DS6, Q5R6G2, Q9ERI5, Q6AYK2, Q6NYC1 5323 RRKRSKSEDMDSVESKRRR Q7TT18 5324 RRKRSR Q99PU7, D3ZHS6, Q92560, A2VDM8 5325 RRPKGKTLQKRKPK Q6ZN17 5326 RRRGFERFGPDNMGRKRK Q63014, Q9DBRO 5327 RRRGKNKVAAQNCRK SeqNLS 5328 RRRKRR Q5FVH8, Q6MZT1, Q08DH5, Q8BQP9 5329 RRRQKQKGGASRRR SeqNLS 5330 RRRREGPRARRRR P08313, P10231 5331 RRTIRLKLVYDKCDRSCKIQKKNRNKCQYC SeqNLS 5332 RFHKCLSVGMSHNAIRFGRMPRSEKAKLKAE RRVPQRKEVSRCRKCRK Q5RJN4, Q32L09, Q8CAK3, Q9NUL5 5333 RVGGRRQAVECIEDLLNEPGQPLD P03255 5334 LSCKRPRP RVVKLRIAP P52639, Q8JMNO 5335 RVVRRR P70278 5336 SKRKTKISRKTR Q5RAY1, 000443 5337 SYVKTVPNRTRTYIKL P21935 5338 TGKNEAKKRKIA P52739, Q8K3J5, Q5RAU9 5339 TLSPASSPSSVSCPVIPASTDESPGSALNI SeqNLS 5340 VSKKORTGKKIH P52739, Q8K3J5, Q5RAU9 5341 SPKKKRKVE 5342 KRTADGSEFESPKKKRKVE 5343 PAAKRVKLD 5344 PKKKRKV 5345 MDSLLMNRRKFLYQFKNVRWAKGRRETYLC 5346 SPKKKRKVEAS 5347 MAPKKKRKVGIHRGVP 5348 KRTADGSEFEKRTADGSEFESPKKKAKVE 5349 KRTADGSEFE 5350 KRTADGSEFESPKKKAKVE 5351 AGKRTADGSEFEKRTADGSEFESPKKKAKVE 4001

In some embodiments, the NLS is a bipartite NLS. A bipartite NLS typically comprises two basic amino acid clusters separated by a spacer sequence (which may be, e.g., about 10 amino acids in length). A monopartite NLS typically lacks a spacer. An example of a bipartite NLS is the nucleoplasmin NLS, having the sequence KR[PAATKKAGQA]KKKK (SEQ ID NO: 5015), wherein the spacer is bracketed. Another exemplary bipartite NLS has the sequence PKKKRKVEGADKRTADGSEFESPKKKRKV (SEQ ID NO: 5016). Exemplary NLSs are described in International Application WO2020051561, which is herein incorporated by reference in its entirety, including for its disclosures regarding nuclear localization sequences.

In certain embodiments, a gene editor system polypeptide (e.g., a gene modifying polypeptide as described herein) further comprises an intracellular localization sequence, e.g., a nuclear localization sequence and/or a nucleolar localization sequence. The nuclear localization sequence and/or nucleolar localization sequence may be amino acid sequences that promote the import of the protein into the nucleus and/or nucleolus, where it can promote integration of heterologous sequence into the genome. In certain embodiments, a gene editor system polypeptide (e.g., (e.g., a gene modifying polypeptide as described herein) further comprises a nucleolar localization sequence. In certain embodiments, the gene modifying polypeptide is encoded on a first RNA, and the template RNA is a second, separate, RNA, and the nucleolar localization signal is encoded on the RNA encoding the gene modifying polypeptide and not on the template RNA. In some embodiments, the nucleolar localization signal is located at the N-terminus, C-terminus, or in an internal region of the polypeptide. In some embodiments, a plurality of the same or different nucleolar localization signals are used. In some embodiments, the nuclear localization signal is less than 5, 10, 25, 50, 75, or 100 amino acids in length. Various polypeptide nucleolar localization signals can be used. For example, Yang et al., Journal of Biomedical Science 22, 33 (2015), describe a nuclear localization signal that also functions as a nucleolar localization signal. In some embodiments, the nucleolar localization signal may also be a nuclear localization signal. In some embodiments, the nucleolar localization signal may overlap with a nuclear localization signal. In some embodiments, the nucleolar localization signal may comprise a stretch of basic residues. In some embodiments, the nucleolar localization signal may be rich in arginine and lysine residues. In some embodiments, the nucleolar localization signal may be derived from a protein that is enriched in the nucleolus. In some embodiments, the nucleolar localization signal may be derived from a protein enriched at ribosomal RNA loci. In some embodiments, the nucleolar localization signal may be derived from a protein that binds rRNA. In some embodiments, the nucleolar localization signal may be derived from MSP58. In some embodiments, the nucleolar localization signal may be a monopartite motif. In some embodiments, the nucleolar localization signal may be a bipartite motif. In some embodiments, the nucleolar localization signal may consist of a multiple monopartite or bipartite motifs. In some embodiments, the nucleolar localization signal may consist of a mix of monopartite and bipartite motifs. In some embodiments, the nucleolar localization signal may be a dual bipartite motif. In some embodiments, the nucleolar localization motif may be a KRASSQALGTIPKRRSSSRFIKRKK (SEQ ID NO: 5017). In some embodiments, the nucleolar localization signal may be derived from nuclear factor-KB-inducing kinase. In some embodiments, the nucleolar localization signal may be an RKKRKKK motif (SEQ ID NO: 5018) (described in Birbach et al., Journal of Cell Science, 117 (3615-3624), 2004).

Evolved Variants of Gene Modifying Polypeptides and Systems

In some embodiments, the invention provides evolved variants of gene modifying polypeptides as described herein. Evolved variants can, in some embodiments, be produced by mutagenizing a reference gene modifying polypeptide, or one of the fragments or domains comprised therein. In some embodiments, one or more of the domains (e.g., the reverse transcriptase domain) is evolved. One or more of such evolved variant domains can, in some embodiments, be evolved alone or together with other domains. An evolved variant domain or domains may, in some embodiments, be combined with unevolved cognate component(s) or evolved variants of the cognate component(s), e.g., which may have been evolved in either a parallel or serial manner.

In some embodiments, the process of mutagenizing a reference gene modifying polypeptide, or fragment or domain thereof, comprises mutagenizing the reference gene modifying polypeptide or fragment or domain thereof. In embodiments, the mutagenesis comprises a continuous evolution method (e.g., PACE) or non-continuous evolution method (e.g., PANCE), e.g., as described herein. In some embodiments, the evolved gene modifying polypeptide, or a fragment or domain thereof, comprises one or more amino acid variations introduced into its amino acid sequence relative to the amino acid sequence of the reference gene modifying polypeptide, or fragment or domain thereof. In embodiments, amino acid sequence variations may include one or more mutated residues (e.g., conservative substitutions, non-conservative substitutions, or a combination thereof) within the amino acid sequence of a reference gene modifying polypeptide, e.g., as a result of a change in the nucleotide sequence encoding the gene modifying polypeptide that results in, e.g., a change in the codon at any particular position in the coding sequence, the deletion of one or more amino acids (e.g., a truncated protein), the insertion of one or more amino acids, or any combination of the foregoing. The evolved variant gene modifying polypeptide may include variants in one or more components or domains of the gene modifying polypeptide (e.g., variants introduced into a reverse transcriptase domain).

In some aspects, the disclosure provides gene modifying polypeptides, systems, kits, and methods using or comprising an evolved variant of a gene modifying polypeptide, e.g., employs an evolved variant of a gene modifying polypeptide or a gene modifying polypeptide produced or producible by PACE or PANCE. In embodiments, the unevolved reference gene modifying polypeptide is a gene modifying polypeptide as disclosed herein.

The term “phage-assisted continuous evolution (PACE),” as used herein, generally refers to continuous evolution that employs phage as viral vectors. Examples of PACE technology have been described, for example, in International PCT Application No. PCT/US 2009/056194, filed Sep. 8, 2009, published as WO 2010/028347 on Mar. 11, 2010; International PCT application, PCT/US2011/066747, filed Dec. 22, 2011, published as WO 2012/088381 on Jun. 28, 2012; U.S. Pat. No. 9,023,594, issued May 5, 2015; U.S. Pat. No. 9,771,574, issued Sep. 26, 2017; U.S. Pat. No. 9,394,537, issued Jul. 19, 2016; International PCT application, PCT/US2015/012022, filed Jan. 20, 2015, published as WO 2015/134121 on Sep. 11, 2015; U.S. Pat. No. 10,179,911, issued Jan. 15, 2019; and International PCT application, PCT/US2016/027795, filed Apr. 15, 2016, published as WO 2016/168631 on Oct. 20, 2016, the entire contents of each of which are incorporated herein by reference.

The term “phage-assisted non-continuous evolution (PANCE),” as used herein, generally refers to non-continuous evolution that employs phage as viral vectors. Examples of PANCE technology have been described, for example, in Suzuki T. et al, Crystal structures reveal an elusive functional domain of pyrrolysyl-tRNA synthetase, Nat Chem Biol. 13(12): 1261-1266 (2017), incorporated herein by reference in its entirety. Briefly, PANCE is a technique for rapid in vivo directed evolution using serial flask transfers of evolving selection phage (SP), which contain a gene of interest to be evolved, across fresh host cells (e.g., E. coli cells). Genes inside the host cell may be held constant while genes contained in the SP continuously evolve. Following phage growth, an aliquot of infected cells may be used to transfect a subsequent flask containing host E. coli. This process can be repeated and/or continued until the desired phenotype is evolved, e.g., for as many transfers as desired.

Methods of applying PACE and PANCE to gene modifying polypeptides may be readily appreciated by the skilled artisan by reference to, inter alia, the foregoing references. Additional exemplary methods for directing continuous evolution of genome-modifying proteins or systems, e.g., in a population of host cells, e.g., using phage particles, can be applied to generate evolved variants of gene modifying polypeptides, or fragments or subdomains thereof. Non-limiting examples of such methods are described in International PCT application, PCT/US2009/056194, filed Sep. 8, 2009, published as WO 2010/028347 on Mar. 11, 2010; International PCT application, PCT/US2011/066747, filed Dec. 22, 2011, published as WO 2012/088381 on Jun. 28, 2012; U.S. Pat. No. 9,023,594, issued May 5, 2015; U.S. Pat. No. 9,771,574, issued Sep. 26, 2017; U.S. Pat. No. 9,394,537, issued Jul. 19, 2016; International PCT application, PCT/US2015/012022, filed Jan. 20, 2015, published as WO 2015/134121 on Sep. 11, 2015; U.S. Pat. No. 10,179,911, issued Jan. 15, 2019; International Application No. PCT/US2019/37216, filed Jun. 14, 2019, International Patent Publication WO 2019/023680, published Jan. 31, 2019, International PCT application, PCT/US2016/027795, filed Apr. 15, 2016, published as WO 2016/168631 on Oct. 20, 2016, and International Patent Publication No. PCT/US2019/47996, filed Aug. 23, 2019, each of which is incorporated herein by reference in its entirety.

In some non-limiting illustrative embodiments, a method of evolution of a evolved variant gene modifying polypeptide, of a fragment or domain thereof, comprises: (a) contacting a population of host cells with a population of viral vectors comprising the gene of interest (the starting gene modifying polypeptide or fragment or domain thereof), wherein: (1) the host cell is amenable to infection by the viral vector; (2) the host cell expresses viral genes required for the generation of viral particles; (3) the expression of at least one viral gene required for the production of an infectious viral particle is dependent on a function of the gene of interest; and/or (4) the viral vector allows for expression of the protein in the host cell, and can be replicated and packaged into a viral particle by the host cell. In some embodiments, the method comprises (b) contacting the host cells with a mutagen, using host cells with mutations that elevate mutation rate (e.g., either by carrying a mutation plasmid or some genome modification—e.g., proofing-impaired DNA polymerase, SOS genes, such as UmuC, UmuD′, and/or RecA, which mutations, if plasmid-bound, may be under control of an inducible promoter), or a combination thereof. In some embodiments, the method comprises (c) incubating the population of host cells under conditions allowing for viral replication and the production of viral particles, wherein host cells are removed from the host cell population, and fresh, uninfected host cells are introduced into the population of host cells, thus replenishing the population of host cells and creating a flow of host cells. In some embodiments, the cells are incubated under conditions allowing for the gene of interest to acquire a mutation. In some embodiments, the method further comprises (d) isolating a mutated version of the viral vector, encoding an evolved gene product (e.g., an evolved variant gene modifying polypeptide, or fragment or domain thereof), from the population of host cells.

The skilled artisan will appreciate a variety of features employable within the above-described framework. For example, in some embodiments, the viral vector or the phage is a filamentous phage, for example, an M13 phage, e.g., an M13 selection phage. In certain embodiments, the gene required for the production of infectious viral particles is the M13 gene III (gIII). In embodiments, the phage may lack a functional gIII, but otherwise comprise gI, gII, gIV, gV, gVI, gVII, gVIII, gIX, and a gX. In some embodiments, the generation of infectious VSV particles involves the envelope protein VSV-G. Various embodiments can use different retroviral vectors, for example, Murine Leukemia Virus vectors, or Lentiviral vectors. In embodiments, the retroviral vectors can efficiently be packaged with VSV-G envelope protein, e.g., as a substitute for the native envelope protein of the virus.

In some embodiments, host cells are incubated according to a suitable number of viral life cycles, e.g., at least 10, at least 20, at least 30, at least 40, at least 50, at least 100, at least 200, at least 300, at least 400, at least, 500, at least 600, at least 700, at least 800, at least 900, at least 1000, at least 1250, at least 1500, at least 1750, at least 2000, at least 2500, at least 3000, at least 4000, at least 5000, at least 7500, at least 10000, or more consecutive viral life cycles, which in on illustrative and non-limiting examples of M13 phage is 10-20 minutes per virus life cycle. Similarly, conditions can be modulated to adjust the time a host cell remains in a population of host cells, e.g., about 10, about 11, about 12, about 13, about 14, about 15, about 16, about 17, about 18, about 19, about 20, about 21, about 22, about 23, about 24, about 25, about 30, about 35, about 40, about 45, about 50, about 55, about 60, about 70, about 80, about 90, about 100, about 120, about 150, or about 180 minutes. Host cell populations can be controlled in part by density of the host cells, or, in some embodiments, the host cell density in an inflow, e.g., 10³ cells/ml, about 10⁴ cells/ml, about 10⁵ cells/ml, about 5-10⁵ cells/ml, about 10⁶ cells/ml, about 5-10⁶ cells/ml, about 10⁷ cells/ml, about 5-10⁷ cells/ml, about 10⁸ cells/ml, about 5-10⁸ cells/ml, about 10⁹ cells/ml, about 5·10⁹ cells/ml, about 10¹⁰ cells/ml, or about 5·10¹⁰ cells/ml.

Inteins

In some embodiments, as described in more detail below, an intein-N (intN) domain may be fused to the N-terminal portion of a first domain of a gene modifying polypeptide described herein, and an intein-C (intC) domain may be fused to the C-terminal portion of a second domain of a gene modifying polypeptide described herein for the joining of the N-terminal portion to the C-terminal portion, thereby joining the first and second domains. In some embodiments, the first and second domains are each independently chosen from a DNA binding domain, an RNA binding domain, an RT domain, and an endonuclease domain.

Inteins can occur as self-splicing protein intron (e.g., peptide), e.g., which ligates flanking N-terminal and C-terminal exteins (e.g., fragments to be joined). An intein may, in some instances, comprise a fragment of a protein that is able to excise itself and join the remaining fragments (the exteins) with a peptide bond in a process known as protein splicing. Inteins are also referred to as “protein introns.” The process of an intein excising itself and joining the remaining portions of the protein is herein termed “protein splicing” or “intein-mediated protein splicing.”

In some embodiments, an intein of a precursor protein (an intein containing protein prior to intein-mediated protein splicing) comes from two genes. Such intein is referred to herein as a split intein (e.g., split intein-N and split intein-C). Accordingly, an intein-based approach may be used to join a first polypeptide sequence and a second polypeptide sequence together. For example, in cyanobacteria, DnaE, the catalytic subunit a of DNA polymerase III, is encoded by two separate genes, dnaE-n and dnaE-c. An intein-N domain, such as that encoded by the dnaE-n gene, when situated as part of a first polypeptide sequence, may join the first polypeptide sequence with a second polypeptide sequence, wherein the second polypeptide sequence comprises an intein-C domain, such as that encoded by the dnaE-c gene. Accordingly, in some embodiments, a protein can be made by providing nucleic acid encoding the first and second polypeptide sequences (e.g., wherein a first nucleic acid molecule encodes the first polypeptide sequence and a second nucleic acid molecule encodes the second polypeptide sequence), and the nucleic acid is introduced into the cell under conditions that allow for production of the first and second polypeptide sequences, and for joining of the first to the second polypeptide sequence via an intein-based mechanism.

Use of inteins for joining heterologous protein fragments is described, for example, in Wood et al., J. Biol. Chem. 289(21); 14512-9 (2014) (incorporated herein by reference in its entirety). For example, when fused to separate protein fragments, the inteins IntN and IntC may recognize each other, splice themselves out, and/or simultaneously ligate the flanking N- and C-terminal exteins of the protein fragments to which they were fused, thereby reconstituting a full-length protein from the two protein fragments.

In some embodiments, a synthetic intein based on the dnaE intein, the Cfa-N (e.g., split intein-N) and Cfa-C (e.g., split intein-C) intein pair, is used. Examples of such inteins have been described, e.g., in Stevens et al., J Am Chem Soc. 2016 Feb. 24; 138(7):2162-5 (incorporated herein by reference in its entirety). Non-limiting examples of intein pairs that may be used in accordance with the present disclosure include: Cfa DnaE intein, Ssp GyrB intein, Ssp DnaX intein, Ter DnaE3 intein, Ter ThyX intein, Rma DnaB intein and Cne Prp8 intein (e.g., as described in U.S. Pat. No. 8,394,604, incorporated herein by reference.

In some embodiments involving a split Cas9, an intein-N domain and an intein-C domain may be fused to the N-terminal portion of the split Cas9 and the C-terminal portion of a split Cas9, respectively, for the joining of the N-terminal portion of the split Cas9 and the C-terminal portion of the split Cas9. For example, in some embodiments, an intein-N is fused to the C-terminus of the N-terminal portion of the split Cas9, i.e., to form a structure of N—[N-terminal portion of the split Cas9]-[intein-N]˜C. In some embodiments, an intein-C is fused to the N-terminus of the C-terminal portion of the split Cas9, i.e., to form a structure of N-[intein-C]˜[C-terminal portion of the split Cas9]-C. The mechanism of intein-mediated protein splicing for joining the proteins the inteins are fused to (e.g., split Cas9) is described in Shah et al., Chem Sci. 2014; 5(1):446-461, incorporated herein by reference. Methods for designing and using inteins are known in the art and described, for example by WO2020051561, WO2014004336, WO2017132580, US20150344549, and US20180127780, each of which is incorporated herein by reference in their entirety.

In some embodiments, a split refers to a division into two or more fragments. In some embodiments, a split Cas9 protein or split Cas9 comprises a Cas9 protein that is provided as an N-terminal fragment and a C-terminal fragment encoded by two separate nucleotide sequences. The polypeptides corresponding to the N-terminal portion and the C-terminal portion of the Cas9 protein may be spliced to form a reconstituted Cas9 protein. In embodiments, the Cas9 protein is divided into two fragments within a disordered region of the protein, e.g., as described in Nishimasu et al., Cell, Volume 156, Issue 5, pp. 935-949, 2014, or as described in Jiang et al. (2016) Science 351: 867-871 and PDB file: 5F9R (each of which is incorporated herein by reference in its entirety). A disordered region may be determined by one or more protein structure determination techniques known in the art, including, without limitation, X-ray crystallography, NMR spectroscopy, electron microscopy (e.g., cryoEM), and/or in silico protein modeling. In some embodiments, the protein is divided into two fragments at any C, T, A, or S, e.g., within a region of SpCas9 between amino acids A292-G364, F445-K483, or E565-T637, or at corresponding positions in any other Cas9, Cas9 variant (e.g., nCas9, dCas9), or other napDNAbp. In some embodiments, protein is divided into two fragments at SpCas9 T310, T313, A456, S469, or C574. In some embodiments, the process of dividing the protein into two fragments is referred to as splitting the protein.

In some embodiments, a protein fragment ranges from about 2-1000 amino acids (e.g., between 2-10, 10-50, 50-100, 100-200, 200-300, 300-400, 400-500, 500-600, 600-700, 700-800, 800-900, or 900-1000 amino acids) in length. In some embodiments, a protein fragment ranges from about 5-500 amino acids (e.g., between 5-10, 10-50, 50-100, 100-200, 200-300, 300-400, or 400-500 amino acids) in length. In some embodiments, a protein fragment ranges from about 20-200 amino acids (e.g., between 20-30, 30-40, 40-50, 50-100, or 100-200 amino acids) in length.

In some embodiments, a portion or fragment of a gene modifying polypeptide is fused to an intein. The nuclease can be fused to the N-terminus or the C-terminus of the intein. In some embodiments, a portion or fragment of a fusion protein is fused to an intein and fused to an AAV capsid protein. The intein, nuclease and capsid protein can be fused together in any arrangement (e.g., nuclease-intein-capsid, intein-nuclease-capsid, capsid-intein-nuclease, etc.). In some embodiments, the N-terminus of an intein is fused to the C-terminus of a fusion protein and the C-terminus of the intein is fused to the N-terminus of an AAV capsid protein.

In some embodiments, an endonuclease domain (e.g., a nickase Cas9 domain) is fused to intein-N and a polypeptide comprising an RT domain is fused to an intein-C.

Exemplary nucleotide and amino acid sequences of intein-N domains and compatible intein-C domains are provided below:

DnaE Intein-N DNA: (SEQ ID NO: 5029) TGCCTGTCATACGAAACCGAGATACTGACAGTAGAATATG GCCTTCTGCCAATCGGGAAGATTGTGGAGAAACGGATAGA ATGCACAGTTTACTCTGTCGATAACAATGGTAACATTTAT ACTCAGCCAGTTGCCCAGTGGCACGACCGGGGAGAGCAGG AAGTATTCGAATACTGTCTGGAGGATGGAAGTCTCATTAG GGCCACTAAGGACCACAAATTTATGACAGTCGATGGCCAG ATGCTGCCTATAGACGAAATCTTTGAGCGAGAGTTGGACC TCATGCGAGTTGACAACCTTCCTAAT DnaE Intein-N Protein: (SEQ ID NO: 5030) CLSYETEILTVEYGLLPIGKIVEKRIECTVYSVDNNGNIY TQPVAQWHDRGEQEVFEYCLEDGSLIRATKDHKFMTVDGQ MLPIDEIFERELDLMRVDNLPN DnaE Intein-C DNA: (SEQ ID NO: 5031) ATGATCAAGATAGCTACAAGGAAGTATCTTGGCAAACAAA ACGTTTATGATATTGGAGTCGAAAGAGATCACAACTTTGC TCTGAAGAACGGATTCATAGCTTCTAAT DnaE Intein-C Protein: (SEQ ID NO: 5032) MIKIATRKYLGKQNVYDIGVERDHNFALKNGFIASN Cfa-N DNA: (SEQ ID NO: 5033) TGCCTGTCTTATGATACCGAGATACTTACCGTTGAATATG GCTTCTTGCCTATTGGAAAGATTGTCGAAGAGAGAATTGA ATGCACAGTATATACTGTAGACAAGAATGGTTTCGTTTAC ACACAGCCCATTGCTCAATGGCACAATCGCGGCGAACAAG AAGTATTTGAGTACTGTCTCGAGGATGGAAGCATCATACG AGCAACTAAAGATCATAAATTCATGACCACTGACGGGCAG ATGTTGCCAATAGATGAGATATTCGAGCGGGGCTTGGATC TCAAACAAGTGGATGGATTGCCA Cfa-N Protein: (SEQ ID NO: 5034) CLSYDTEILTVEYGFLPIGKIVEERIECTVYTVDKNGFVY TQPIAQWHNRGEQEVFEYCLEDGSIIRATKDHKFMTTDGQ MLPIDEIFERGLDLKQVDGLP Cfa-C DNA: (SEQ ID NO: 5035) ATGAAGAGGACTGCCGATGGATCAGAGTTTGAATCTCCCA AGAAGAAGAGGAAAGTAAAGATAATATCTCGAAAAAGTCT TGGTACCCAAAATGTCTATGATATTGGAGTGGAGAAAGAT CACAACTTCCTTCTCAAGAACGGTCTCGTAGCCAGCAAC Cfa-C Protein: (SEQ ID NO: 5036) MKRTADGSEFESPKKKRKVKIISRKSLGTQNVYDIGVEKD HNFLLKNGLVASN

Additional Domains

The gene modifying polypeptide can bind a target DNA sequence and template nucleic acid (e.g., template RNA), nick the target site, and write (e.g., reverse transcribe) the template into DNA, resulting in a modification of the target site. In some embodiments, additional domains may be added to the polypeptide to enhance the efficiency of the process. In some embodiments, the gene modifying polypeptide may contain an additional DNA ligation domain to join reverse transcribed DNA to the DNA of the target site. In some embodiments, the polypeptide may comprise a heterologous RNA-binding domain. In some embodiments, the polypeptide may comprise a domain having 5′ to 3′ exonuclease activity (e.g., wherein the 5′ to 3′ exonuclease activity increases repair of the alteration of the target site, e.g., in favor of alteration over the original genomic sequence). In some embodiments, the polypeptide may comprise a domain having 3′ to 5′ exonuclease activity, e.g., proof-reading activity. In some embodiments, the writing domain, e.g., RT domain, has 3′ to 5′ exonuclease activity, e.g., proof-reading activity.

Template Nucleic Acids

The gene modifying systems described herein can modify a host target DNA site using a template nucleic acid sequence. In some embodiments, the gene modifying systems described herein transcribe an RNA sequence template into host target DNA sites by target-primed reverse transcription (TPRT). By modifying DNA sequence(s) via reverse transcription of the RNA sequence template directly into the host genome, the gene modifying system can insert an object sequence into a target genome without the need for exogenous DNA sequences to be introduced into the host cell (unlike, for example, CRISPR systems), as well as eliminate an exogenous DNA insertion step. The gene modifying system can also delete a sequence from the target genome or introduce a substitution using an object sequence. Therefore, the gene modifying system provides a platform for the use of customized RNA sequence templates containing object sequences, e.g., sequences comprising heterologous gene coding and/or function information.

In some embodiments, the template nucleic acid comprises one or more sequence (e.g., 2 sequences) that binds the gene modifying polypeptide.

In some embodiments a system or method described herein comprises a single template nucleic acid (e.g., template RNA). In some embodiments a system or method described herein comprises a plurality of template nucleic acids (e.g., template RNAs). For example, a system described herein comprises a first RNA comprising (e.g., from 5′ to 3′) a sequence that binds the gene modifying polypeptide (e.g., the DNA-binding domain and/or the endonuclease domain, e.g., a gRNA) and a sequence that binds a target site (e.g., a second strand of a site in a target genome), and a second RNA (e.g., a template RNA) comprising (e.g., from 5′ to 3′) optionally a sequence that binds the gene modifying polypeptide (e.g., that specifically binds the RT domain), a heterologous object sequence, and a PBS sequence. In some embodiments, when the system comprises a plurality of nucleic acids, each nucleic acid comprises a conjugating domain. In some embodiments, a conjugating domain enables association of nucleic acid molecules, e.g., by hybridization of complementary sequences. For example, in some embodiments a first RNA comprises a first conjugating domain and a second RNA comprises a second conjugating domain, and the first and second conjugating domains are capable of hybridizing to one another, e.g., under stringent conditions. In some embodiments, the stringent conditions for hybridization include hybridization in 4× sodium chloride/sodium citrate (SSC), at about 65° C., followed by a wash in 1×SSC, at about 65° C.

In some embodiments, the template nucleic acid comprises RNA. In some embodiments, the template nucleic acid comprises DNA (e.g., single stranded or double stranded DNA).

In some embodiments, the template nucleic acid comprises one or more (e.g., 2) homology domains that have homology to the target sequence. In some embodiments, the homology domains are about 10-20, 20-50, or 50-100 nucleotides in length.

In some embodiments, a template RNA can comprise a gRNA sequence, e.g., to direct the gene modifying polypeptide to a target site of interest. In some embodiments, a template RNA comprises (e.g., from 5′ to 3′) (i) optionally a gRNA spacer that binds a target site (e.g., a second strand of a site in a target genome), (ii) optionally a gRNA scaffold that binds a polypeptide described herein (e.g., a gene modifying polypeptide or a Cas polypeptide), (iii) a heterologous object sequence comprising a mutation region (optionally the heterologous object sequence comprises, from 5′ to 3′, a first homology region, a mutation region, and a second homology region), and (iv) a primer binding site (PBS) sequence comprising a 3′ target homology domain.

The template nucleic acid (e.g., template RNA) component of a genome editing system described herein typically is able to bind the gene modifying polypeptide of the system. In some embodiments the template nucleic acid (e.g., template RNA) has a 3′ region that is capable of binding a gene modifying polypeptide. The binding region, e.g., 3′ region, may be a structured RNA region, e.g., having at least 1, 2 or 3 hairpin loops, capable of binding the gene modifying polypeptide of the system. The binding region may associate the template nucleic acid (e.g., template RNA) with any of the polypeptide modules. In some embodiments, the binding region of the template nucleic acid (e.g., template RNA) may associate with an RNA-binding domain in the polypeptide. In some embodiments, the binding region of the template nucleic acid (e.g., template RNA) may associate with the reverse transcription domain of the gene modifying polypeptide (e.g., specifically bind to the RT domain). In some embodiments, the template nucleic acid (e.g., template RNA) may associate with the DNA binding domain of the polypeptide, e.g., a gRNA associating with a Cas9-derived DNA binding domain. In some embodiments, the binding region may also provide DNA target recognition, e.g., a gRNA hybridizing to the target DNA sequence and binding the polypeptide, e.g., a Cas9 domain. In some embodiments, the template nucleic acid (e.g., template RNA) may associate with multiple components of the polypeptide, e.g., DNA binding domain and reverse transcription domain.

In some embodiments the template RNA has a poly-A tail at the 3′ end. In some embodiments the template RNA does not have a poly-A tail at the 3′ end.

In some embodiments, a template RNA may be customized to correct a given mutation in the genomic DNA of a target cell (e.g., ex vivo or in vivo, e.g., in a target tissue or organ, e.g., in a subject). For example, the mutation may be a disease-associated mutation relative to the wild-type sequence. Without wishing to be bound by theory, any given target site and edit will have a large number of possible template RNA molecules for use in a gene modifying system that will result in a range of editing efficiencies and fidelities. To partially reduce this screening burden, sets of empirical parameters help ensure optimal initial in silico designs of template RNAs or portions thereof. As a non-limiting illustrative example, for a selected mutation, the following design parameters may be employed. In some embodiments, design is initiated by acquiring approximately 500 bp (e.g., up to 50, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, or 700 bp, and optionally at least 20, 30, 40, 50, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, or 650 bp) flanking sequence on either side of the mutation to serve as the target region. In some embodiments, a template nucleic acid comprises a gRNA. In some embodiments, a gRNA comprises a sequence (e.g., a CRISPR spacer) that binds a target site. In some embodiments, the sequence (e.g., a CRISPR spacer) that binds a target site for use in targeting a template nucleic acid to a target region is selected by considering the particular gene modifying polypeptide (e.g., endonuclease domain or writing domain, e.g., comprising a CRISPR/Cas domain) being used (e.g., for Cas9, a protospacer-adjacent motif (PAM) of NGG immediately 3′ of a 20 nucleotide gRNA binding region). In some embodiments, the CRISPR spacer is selected by ranking first by whether the PAM will be disrupted by the gene modifying system induced edit. In some embodiments, disruption of the PAM may increase edit efficiency. In some embodiments, the PAM can be disrupted by also introducing (e.g., as part of or in addition to another modification to a target site in genomic DNA) a silent mutation (e.g., a mutation that does not alter an amino acid residue encoded by the target nucleic acid sequence, if any) in the target site during gene modification. In some embodiments, the CRISPR spacer is selected by ranking sequences by the proximity of their corresponding genomic site to the desired edit location. In some embodiments, the gRNA comprises a gRNA scaffold. In some embodiments, the gRNA scaffold used may be a standard scaffold (e.g., for Cas9, 5′-GTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGG CACCGAGTCGGTGC-3′; SEQ ID NO: 11,003), or may contain one or more nucleotide substitutions. In some embodiments, the heterologous object sequence has at least 90% identity, e.g., at least 90%, 95%, 98%, 99%, or 100% identity, or comprises no more than 1, 2, 3, 4, or 5 positions of non-identity to the target site 3′ of the first strand nick (e.g., immediately 3′ of the first strand nick or up to 1, 2, 3, 4, or 5 nucleotides 3′ of the first strand nick), with the exception of any insertion, substitution, or deletion that may be written into the target site by the gene modifying. In some embodiments, the 3′ target homology domain contains at least 90% identity, e.g., at least 90%, 95%, 98%, 99%, or 100% identity, or comprises no more than 1, 2, 3, 4, or 5 positions of non-identity to the target site 5′ of the first strand nick (e.g., immediately 5′ of the first strand nick or up to 1, 2, 3, 4, or 5 nucleotides 3′ of the first strand nick).

In some embodiments, the template nucleic acid is a template RNA. In some embodiments, the template RNA comprises one or more modified nucleotides. For example, in some embodiments, the template RNA comprises one or more deoxyribonucleotides. In some embodiments, regions of the template RNA are replaced by DNA nucleotides, e.g., to enhance stability of the molecule. For example, the 3′ end of the template may comprise DNA nucleotides, while the rest of the template comprises RNA nucleotides that can be reverse transcribed. For instance, in some embodiments, the heterologous object sequence is primarily or wholly made up of RNA nucleotides (e.g., at least 90%, 95%, 98%, or 99% RNA nucleotides). In some embodiments, the PBS sequence is primarily or wholly made up of DNA nucleotides (e.g., at least 90%, 95%, 98%, or 99% DNA nucleotides). In other embodiments, the heterologous object sequence for writing into the genome may comprise DNA nucleotides. In some embodiments, the DNA nucleotides in the template are copied into the genome by a domain capable of DNA-dependent DNA polymerase activity. In some embodiments, the DNA-dependent DNA polymerase activity is provided by a DNA polymerase domain in the polypeptide. In some embodiments, the DNA-dependent DNA polymerase activity is provided by a reverse transcriptase domain that is also capable of DNA-dependent DNA polymerization, e.g., second strand synthesis. In some embodiments, the template molecule is composed of only DNA nucleotides.

In some embodiments, a system described herein comprises two nucleic acids which together comprise the sequences of a template RNA described herein. In some embodiments, the two nucleic acids are associated with each other non-covalently, e.g., directly associated with each other (e.g., via base pairing), or indirectly associated as part of a complex comprising one or more additional molecule.

A template RNA described herein may comprise, from 5′ to 3′: (1) a gRNA spacer; (2) a gRNA scaffold; (3) heterologous object sequence (4) a primer binding site (PBS) sequence. Each of these components is now described in more detail.

gRNA Spacer and gRNA Scaffold

A template RNA described herein may comprise a gRNA spacer that directs the gene modifying system to a target nucleic acid, and a gRNA scaffold that promotes association of the template RNA with the Cas domain of the gene modifying polypeptide. The systems described herein can also comprise a gRNA that is not part of a template nucleic acid. For example, a gRNA that comprises a gRNA spacer and gRNA scaffold, but not a heterologous object sequence or a PBS sequence, can be used, e.g., to induce second strand nicking, e.g., as described in the section herein entitled “Second Strand Nicking”.

In some embodiments, the gRNA is a short synthetic RNA composed of a scaffold sequence that participates in CRISPR-associated protein binding and a user-defined ˜20 nucleotide targeting sequence for a genomic target. The structure of a complete gRNA was described by Nishimasu et al. Cell 156, P935-949 (2014). The gRNA (also referred to as sgRNA for single-guide RNA) consists of crRNA- and tracrRNA-derived sequences connected by an artificial tetraloop. The crRNA sequence can be divided into guide (20 nt) and repeat (12 nt) regions, whereas the tracrRNA sequence can be divided into anti-repeat (14 nt) and three tracrRNA stem loops (Nishimasu et al. Cell 156, P935-949 (2014)). In practice, guide RNA sequences are generally designed to have a length of between 17-24 nucleotides (e.g., 19, 20, or 21 nucleotides) and be complementary to a targeted nucleic acid sequence. Custom gRNA generators and algorithms are available commercially for use in the design of effective guide RNAs. In some embodiments, the gRNA comprises two RNA components from the native CRISPR system, e.g. crRNA and tracrRNA. As is well known in the art, the gRNA may also comprise a chimeric, single guide RNA (sgRNA) containing sequence from both a tracrRNA (for binding the nuclease) and at least one crRNA (to guide the nuclease to the sequence targeted for editing/binding). Chemically modified sgRNAs have also been demonstrated to be effective for use with CRISPR-associated proteins; see, for example, Hendel et al. (2015) Nature Biotechnol., 985-991. In some embodiments, a gRNA spacer comprises a nucleic acid sequence that is complementary to a DNA sequence associated with a target gene.

In some embodiments, the region of the template nucleic acid, e.g., template RNA, comprising the gRNA adopts an underwound ribbon-like structure of gRNA bound to target DNA (e.g., as described in Mulepati et al. Science 19 Sep. 2014:Vol. 345, Issue 6203, pp. 1479-1484). Without wishing to be bound by theory, this non-canonical structure is thought to be facilitated by rotation of every sixth nucleotide out of the RNA-DNA hybrid. Thus, in some embodiments, the region of the template nucleic acid, e.g., template RNA, comprising the gRNA may tolerate increased mismatching with the target site at some interval, e.g., every sixth base. In some embodiments, the region of the template nucleic acid, e.g., template RNA, comprising the gRNA comprising homology to the target site may possess wobble positions at a regular interval, e.g., every sixth base, that do not need to base pair with the target site.

In some embodiments, the template nucleic acid (e.g., template RNA) has at least 15, 16, 17, 18, 19, 20, 21, 22, 23, or 24 bases of at least 80%, 85%, 90%, 95%, 99%, or 100% homology to the target site, e.g., at the 5′ end, e.g., comprising a gRNA spacer sequence of length appropriate to the Cas9 domain of the gene modifying polypeptide (Table 8).

Table 12 provides parameters to define components for designing gRNA and/or Template RNAs to apply Cas variants listed in Table 8 for gene modifying. The cut site indicates the validated or predicted protospacer adjacent motif (PAM) requirements, validated or predicted location of cut site (relative to the most upstream base of the PAM site). The gRNA for a given enzyme can be assembled by concatenating the crRNA, Tetraloop, and tracrRNA sequences, and further adding a 5′ spacer of a length within Spacer (min) and Spacer (max) that matches a protospacer at a target site. Further, the predicted location of the ssDNA nick at the target is important for designing a PBS sequence of a Template RNA that can anneal to the sequence immediately 5′ of the nick in order to initiate target primed reverse transcription. In some embodiments, a gRNA scaffold described herein comprises a nucleic acid sequence comprising, in the 5′ to 3′ direction, a crRNA of Table 12, a tetraloop from the same row of Table 12, and a tracrRNA from the same row of Table 12, or a sequence having at least 70%, 80%, 85%, 90%, 95%, or 99% identity thereto. In some embodiments, the gRNA or template RNA comprising the scaffold further comprises a gRNA spacer having a length within the Spacer (min) and Spacer (max) indicated in the same row of Table 12. In some embodiments, the gRNA or template RNA having a sequence according to Table 12 is comprised by a system that further comprises a gene modifying polypeptide, wherein the gene modifying polypeptide comprises a Cas domain described in the same row of Table 12.

TABLE 12 Parameters to define components for designing gRNA and/or Template RNAs to apply Cas variants listed in Table 8 in gene modifying systems Spacer Spacer SEQ ID Tetra- SEQ ID Variant PAM(s) Cut Tier (min) (max) crRNA NO: loop tracrRNA NO: Nme2Cas9 NNNNCC −3 1 22 24 GTTGTAGC 10,051 GAAA CGAAATGAGA 10,151 TCCCTTTCT ACCGTTGCTA CATTTCG CAATAAGGCC GTCTGAAAAG ATGTGCCGCA ACGCTCTGCC CCTTAAAGCT TCTGCTTTAA GGGGCATCGT TTA PpnCas9 NNNNRTT 1 21 24 GTTGTAGC 10,052 GAAA GCGAAATGAA 10,152 TCCCTTTTT AAACGTTGTT CATTTCGC ACAATAAGAG ATGAATTTCT CGCAAAGCTC TGCCTCTTGA AATTTCGGTT TCAAGAGGCA TC SauCas9 NNGRR; −3 1 21 23 GTTTTAGT 10,053 GAAA CAGAATCTAC 10,153 NNGRRT ACTCTG TAAAACAAGG CAAAATGCCG TGTTTATCTC GTCAACTTGT TGGCGAGA SauCas9-KKH NNNRR; −3 1 21 21 GTTTTAGT 10,054 GAAA CAGAATCTAC 10,154 NNNRRT ACTCTG TAAAACAAGG CAAAATGCCG TGTTTATCTC GTCAACTTGT TGGCGAGA SauriCas9 NNGG −3 1 21 21 GTTTTAGT 10,055 GAAA CAGAATCTAC 10,155 ACTCTG TAAAACAAGG CAAAATGCCG TGTTTATCTC GTCAACTTGT TGGCGAGA SauriCas9-KKH NNRG −3 1 21 21 GTTTTAGT 10,056 GAAA CAGAATCTAC 10,156 ACTCTG TAAAACAAGG CAAAATGCCG TGTTTATCTC GTCAACTTGT TGGCGAGA ScaCas9-Sc++ NNG −3 1 20 20 GTTTTAGA 10,057 GAAA TAGCAAGTTA 10,157 GCTA AAATAAGGCT AGTCCGTTAT CAACTTGAAA AAGTGGCACC GAGTCGGTGC SpyCas9 NGG −3 1 20 20 GTTTTAGA 10,058 GAAA TAGCAAGTTA 10,158 GCTA AAATAAGGCT AGTCCGTTAT CAACTTGAAA AAGTGGCACC GAGTCGGTGC SpyCas9_i_v1 NGG −3 1 20 20 GTTTTAGA 10057 GAAA TAGCAAGTTA 10,193 GCTA AAATAAGGCT AGTCCGTTAT CAACTTGGAC TTCGGTCCAA GTGGCACCGA GTCGGTGC SpyCas9_i_v2 NGG −3 1 20 20 GTTTTAGA 10057 GAAA TAGCAAGTTA 10,194 GCTA AAATAAGGCT AGTCCGTTAT CAACTTGGAG CTTGCTCCAA GTGGCACCGA GTCGGTGC SpyCas9_i_v3 NGG −3 1 20 20 GTTTTAGA 10057 GAAA GTTTTAGAGC 10,195 GCTA TAGAAATAGC AAGTTAAAAT AAGGCTAGTC CGTTATCGAC TTGAAAAAGT CGCACCGAGT CGGTGC SpyCas9-NG NG −3 1 20 20 GTTTTAGA 10,059 GAAA TAGCAAGTTA 10,159 (NGG = GCTA AAATAAGGCT NGA = AGTCCGTTAT NGT > CAACTTGAAA NGC) AAGTGGCACC GAGTCGGTGC SpyCas9-SpRY NRN > −3 1 20 20 GTTTTAGA 10,060 GAAA TAGCAAGTTA 10,160 NYN GCTA AAATAAGGCT AGTCCGTTAT CAACTTGAAA AAGTGGCACC GAGTCGGTGC St1Cas9 NNAGAA −3 1 20 20 GTCTTTGTA 10,061 GTAC CAGAAGCTAC 10,161 W > NNAG CTCTG AAAGATAAGG GAW = NN CTTCATGCCG GGAAW AAATCAACAC CCTGTCATTT TATGGCAGGG TGTTTT BlatCas9 NNNNCN −3 1 19 23 GCTATAGT 10,062 GAAA GGTAAGTTGC 10,162 AA > TCCTTACT TATAGTAAGG NNNN GCAACAGACC CNDD > CGAGGCGTTG NNNNC GGGATCGCCT AGCCCGTGTT TACGGGCTCT CCCCATATTC AAAATAATGA CAGACGAGCA CCTTGGAGCA TTTATCTCCG AGGTGCT cCas9-v16 NNVACT; −3 2 21 21 GTCTTAGT 10,063 GAAA CAGAATCTAC 10,163 NNVATGM; ACTCTG TAAGACAAGG NNVATT; CAAAATGCCG NNVGCT; TGTTTATCTC NNVGTG; GTCAACTTGT NNVGTT TGGCGAGA cCas9-v17 NNVRRN −3 2 21 21 GTCTTAGT 10,064 GAAA CAGAATCTAC 10,164 ACTCTG TAAGACAAGG CAAAATGCCG TGTTTATCTC GTCAACTTGT TGGCGAGA cCas9-v21 NNVACT; −3 2 21 21 GTCTTAGT 10,065 GAAA CAGAATCTAC 10,165 NNVATGM; ACTCTG TAAGACAAGG NNVATT; CAAAATGCCG NNVGCT; TGTTTATCTC NNVGTG; GTCAACTTGT NNVGTT TGGCGAGA cCas9-v42 NNVRRN −3 2 21 21 GTCTTAGT 10,066 GAAA CAGAATCTAC 10,166 ACTCTG TAAGACAAGG CAAAATGCCG TGTTTATCTC GTCAACTTGT TGGCGAGA CdiCas9 NNRHHHY; 2 22 22 ACTGGGGT 10,067 GAAA CTGAACCTCA 10,167 NNRAAAY TCAG GTAAGCATTG GCTCGTTTCC AATGTTGATT GCTCCGCCGG TGCTCCTTAT TTTTAAGGGC GCCGGC CjeCas9 NNNNRYA −3 2 21 23 GTTTTAGTC 10,068 GAAA AGGGACTAAA 10,168 C CCT ATAAAGAGTT TGCGGGACTC TGCGGGGTTA CAATCCCCTA AAACCGC GeoCas9 NNNNCRA 2 21 23 GTCATAGT 10,069 GAAA TCAGGGTTAC 10,169 A TCCCCTGA TATGATAAGG GCTTTCTGCC TAAGGCAGAC TGACCCGCGG CGTTGGGGAT CGCCTGTCGC CCGCTTTTGG CGGGCATTCC CCATCCTT iSpyMacCas9 NAAN −3 2 19 21 GTTTTAGA 10,070 GAAA TAGCAAGTTA 10,170 GCTA AAATAAGGCT AGTCCGTTAT CAACTTGAAA AAGTGGCACC GAGTCGGTGC NmeCas9 NNNNGA −3 2 20 24 GTTGTAGC 10,071 GAAA CGAAATGAGA 10,171 YT; NNNN TCCCTTTCT ACCGTTGCTA GYTT; NN CATTTCG CAATAAGGCC NNGAYA; GTCTGAAAAG NNNNGTC ATGTGCCGCA T ACGCTCTGCC CCTTAAAGCT TCTGCTTTAA GGGGCATCGT TTA ScaCas9 NNG −3 2 20 20 GTTTTAGA 10,072 GAAA TAGCAAGTTA 10,172 GCTA AAATAAGGCT AGTCCGTTAT CAACTTGAAA AAGTGGCACC GAGTCGGTGC ScaCas9-HiFi- NNG −3 2 20 20 GTTTTAGA 10,073 GAAA TAGCAAGTTA 10,173 Sc++ GCTA AAATAAGGCT AGTCCGTTAT CAACTTGAAA AAGTGGCACC GAGTCGGTGC SpyCas9-3var- NRRH −3 2 20 20 GTTTAAGA 10,074 GAAA CAGCATAGCA 10,174 NRRH GCTATGCT AGTTTAAATA G AGGCTAGTCC GTTATCAACT TGAAAAAGTG GCACCGAGTC GGTGC SpyCas9-3var- NRTH −3 2 20 20 GTTTAAGA 10,075 GAAA CAGCATAGCA 10,175 NRTH GCTATGCT AGTTTAAATA G AGGCTAGTCC GTTATCAACT TGAAAAAGTG GCACCGAGTC GGTGC SpyCas9-3var- NRCH −3 2 20 20 GTTTAAGA 10,076 GAAA CAGCATAGCA 10,176 NRCH GCTATGCT AGTTTAAATA G AGGCTAGTCC GTTATCAACT TGAAAAAGTG GCACCGAGTC GGTGC SpyCas9-HF1 NGG −3 2 20 20 GTTTTAGA 10,077 GAAA TAGCAAGTTA 10,177 GCTA AAATAAGGCT AGTCCGTTAT CAACTTGAAA AAGTGGCACC GAGTCGGTGC SpyCas9- NAAG −3 2 20 20 GTTTTAGA 10,078 GAAA TAGCAAGTTA 10,178 QQR1 GCTA AAATAAGGCT AGTCCGTTAT CAACTTGAAA AAGTGGCACC GAGTCGGTGC SpyCas9-SpG NGN −3 2 20 20 GTTTTAGA 10,079 GAAA TAGCAAGTTA 10,179 GCTA AAATAAGGCT AGTCCGTTAT CAACTTGAAA AAGTGGCACC GAGTCGGTGC SpyCas9-VQR NGAN −3 2 20 20 GTTTTAGA 10,080 GAAA TAGCAAGTTA 10,180 GCTA AAATAAGGCT AGTCCGTTAT CAACTTGAAA AAGTGGCACC GAGTCGGTGC SpyCas9-VRER NGCG −3 2 20 20 GTTTTAGA 10,081 GAAA TAGCAAGTTA 10,181 GCTA AAATAAGGCT AGTCCGTTAT CAACTTGAAA AAGTGGCACC GAGTCGGTGC SpyCas9-xCas NG; GAA; −3 2 20 20 GTTTAAGA 10,082 GAAA CAGCATAGCA 10,182 GAT GCTATGCT AGTTTAAATA G AGGCTAGTCC GTTATCAACT TGAAAAAGTG GCACCGAGTC GGTGC SpyCas9-xCas- NG −3 2 20 20 GTTTAAGA 10,083 GAAA CAGCATAGCA 10,183 NG GCTATGCT AGTTTAAATA G AGGCTAGTCC GTTATCAACT TGAAAAAGTG GCACCGAGTC GGTGC St1Cas9- NNACAA −3 2 20 20 GTCTTTGTA 10,084 GTAC CAGAAGCTAC 10,184 CNRZ1066 CTCTG AAAGATAAGG CTTCATGCCG AAATCAACAC CCTGTCATTT TATGGCAGGG TGTTTT St1Cas9- NNGCAA −3 2 20 20 GTCTTTGTA 10,085 GTAC CAGAAGCTAC 10,185 LMG1831 CTCTG AAAGATAAGG CTTCATGCCG AAATCAACAC CCTGTCATTT TATGGCAGGG TGTTTT St1Cas9- NNAAAA −3 2 20 20 GTCTTTGTA 10,086 GTAC CAGAAGCTAC 10,186 MTH17CL396 CTCTG AAAGATAAGG CTTCATGCCG AAATCAACAC CCTGTCATTT TATGGCAGGG TGTTTT St1Cas9- NNGAAA −3 2 20 20 GTCTTTGTA 10,087 GTAC CAGAAGCTAC 10,187 TH1477 CTCTG AAAGATAAGG CTTCATGCCG AAATCAACAC CCTGTCATTT TATGGCAGGG TGTTTT sRGN3.1 NNGG 1 21 23 GTTTTAGT 10,088 GAAA CAGAATCTAC 10,188 ACTCTG TGAAACAAGA CAATATGTCG TGTTTATCCC ATCAATTTAT TGGTGGGATT TT SRGN3.3 NNGG 1 21 23 GTTTTAGT 10,089 GAAA CAGAATCTAC 10,189 ACTCTG TGAAACAAGA CAATATGTCG TGTTTATCCC ATCAATTTAT TGGTGGGATT TT

Herein, when an RNA sequence (e.g., a template RNA sequence) is said to comprise a particular sequence (e.g., a sequence of Table 12 or a portion thereof) that comprises thymine (T), it is of course understood that the RNA sequence may (and frequently does) comprise uracil (U) in place of T. For instance, the RNA sequence may comprise U at every position shown as T in the sequence in Table 12. More specifically, the present disclosure provides an RNA sequence according to every gRNA scaffold sequence of Table 12, wherein the RNA sequence has a U in place of each T in the sequence in Table 12. Additionally, it is understood that terminal Us and Ts may optionally be added or removed from tracrRNA sequences and may be modified or unmodified when provided as RNA. Without wishing to be bound by example, versions of gRNA scaffold sequences alternative to those exemplified in Table 12 may also function with the different Cas9 enzymes or derivatives thereof exemplified in Table 8, e.g., alternate gRNA scaffold sequences with nucleotide additions, substitutions, or deletions, e.g., sequences with stem-loop structures added or removed. It is contemplated herein that the gRNA scaffold sequences represent a component of gene modifying systems that can be similarly optimized for a given system, Cas-RT fusion polypeptide, indication, target mutation, template RNA, or delivery vehicle.

Heterologous Object Sequence

A template RNA described herein may comprise a heterologous object sequence that the gene modifying polypeptide can use as a template for reverse transcription, to write a desired sequence into the target nucleic acid. In some embodiments, the heterologous object sequence comprises, from 5′ to 3′, a post-edit homology region, the mutation region, and a pre-edit homology region. Without wishing to be bound by theory, an RT performing reverse transcription on the template RNA first reverse transcribes the pre-edit homology region, then the mutation region, and then the post-edit homology region, thereby creating a DNA strand comprising the desired mutation with a homology region on either side.

In some embodiments, the heterologous object sequence is at least 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 120, 140, 160, 180, 200, 500, or 1,000 nucleotides (nts) in length, or at least 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 5.5, 6, 6.5, 7, 7.5, 8, 8.5, 9, 9.5, or 10 kilobases in length. In some embodiments, the heterologous object sequence is no more than 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 120, 140, 160, 180, 200, 500, 1,000, or 2000 nucleotides (nts) in length, or no more than 20, 15, 10, 9, 8, 7, 6, 5, 4, or 3 kilobases in length. In some embodiments, the heterologous object sequence is 30-1000, 40-1000, 50-1000, 60-1000, 70-1000, 74-1000, 75-1000, 76-1000, 77-1000, 78-1000, 79-1000, 80-1000, 85-1000, 90-1000, 100-1000, 120-1000, 140-1000, 160-1000, 180-1000, 200-1000, 500-1000, 30-500, 40-500, 50-500, 60-500, 70-500, 74-500, 75-500, 76-500, 77-500, 78-500, 79-500, 80-500, 85-500, 90-500, 100-500, 120-500, 140-500, 160-500, 180-500, 200-500, 30-200, 40-200, 50-200, 60-200, 70-200, 74-200, 75-200, 76-200, 77-200, 78-200, 79-200, 80-200, 85-200, 90-200, 100-200, 120-200, 140-200, 160-200, 180-200, 30-100, 40-100, 50-100, 60-100, 70-100, 74-100, 75-100, 76-100, 77-100, 78-100, 79-100, 80-100, 85-100, or 90-100 nucleotides (nts) in length, or 1-20, 1-15, 1-10, 1-9, 1-8, 1-7, 1-6, 1-5, 1-4, 1-3, 1-2, 2-20, 2-15, 2-10, 2-9, 2-8, 2-7, 2-6, 2-5, 2-4, 2-3, 3-20, 3-15, 3-10, 3-9, 3-8, 3-7, 3-6, 3-5, 3-4, 4-20, 4-15, 4-10, 4-9, 4-8, 4-7, 4-6, 4-5, 5-20, 5-15, 5-10, 5-9, 5-8, 5-7, 5-6, 6-20, 6-15, 6-10, 6-9, 6-8, 6-7, 7-20, 7-15, 7-10, 7-9, 7-8, 8-20, 8-15, 8-10, 8-9, 9-20, 9-15, 9-10, 10-15, 10-20, or 15-20 kilobases in length. In some embodiments, the heterologous object sequence is 10-100, 10-90, 10-80, 10-70, 10-60, 10-50, 10-40, 10-30, or 10-20 nt in length, e.g., 10-80, 10-50, or 10-20 nt in length, e.g., about 10-20 nt in length. In some embodiments, the heterologous object sequence is 8-30, 9-25, 10-20, 11-16, or 12-15 nucleotides in length, e.g., is 11-16 nt in length. Without wishing to be bound by theory, in some embodiments, a larger insertion size, larger region of editing (e.g., the distance between a first edit/substitution and a second edit/substitution in the target region), and/or greater number of desired edits (e.g., mismatches of the heterologous object sequence to the target genome), may result in a longer optimal heterologous object sequence.

In certain embodiments, the template nucleic acid comprises a customized RNA sequence template which can be identified, designed, engineered and constructed to contain sequences altering or specifying host genome function, for example by introducing a heterologous coding region into a genome; affecting or causing exon structure/alternative splicing, e.g., leading to exon skipping of one or more exons; causing disruption of an endogenous gene, e.g., creating a genetic knockout; causing transcriptional activation of an endogenous gene; causing epigenetic regulation of an endogenous DNA; causing up-regulation of one or more operably linked genes, e.g., leading to gene activation or overexpression; causing down-regulation of one or more operably linked genes, e.g., creating a genetic knock-down; etc. In certain embodiments, a customized RNA sequence template can be engineered to contain sequences coding for exons and/or transgenes, provide binding sites for transcription factor activators, repressors, enhancers, etc., and combinations thereof. In some embodiments, a customized template can be engineered to encode a nucleic acid or peptide tag to be expressed in an endogenous RNA transcript or endogenous protein operably linked to the target site. In other embodiments, the coding sequence can be further customized with splice donor sites, splice acceptor sites, or poly-A tails.

The template nucleic acid (e.g., template RNA) of the system typically comprises an object sequence (e.g., a heterologous object sequence) for writing a desired sequence into a target DNA. The object sequence may be coding or non-coding. The template nucleic acid (e.g., template RNA) can be designed to result in insertions, mutations, or deletions at the target DNA locus. In some embodiments, the template nucleic acid (e.g., template RNA) may be designed to cause an insertion in the target DNA. For example, the template nucleic acid (e.g., template RNA) may contain a heterologous sequence, wherein the reverse transcription will result in insertion of the heterologous sequence into the target DNA. In other embodiments, the RNA template may be designed to introduce a deletion into the target DNA. For example, the template nucleic acid (e.g., template RNA) may match the target DNA upstream and downstream of the desired deletion, wherein the reverse transcription will result in the copying of the upstream and downstream sequences from the template nucleic acid (e.g., template RNA) without the intervening sequence, e.g., causing deletion of the intervening sequence. In other embodiments, the template nucleic acid (e.g., template RNA) may be designed to introduce an edit into the target DNA. For example, the template RNA may match the target DNA sequence with the exception of one or more nucleotides, wherein the reverse transcription will result in the copying of these edits into the target DNA, e.g., resulting in mutations, e.g., transition or transversion mutations.

In some embodiments, writing of an object sequence into a target site results in the substitution of nucleotides, e.g., where the full length of the object sequence corresponds to a matching length of the target site with one or more mismatched bases. In some embodiments, a heterologous object sequence may be designed such that a combination of sequence alterations may occur, e.g., a simultaneous addition and deletion, addition and substitution, or deletion and substitution.

In some embodiments, the heterologous object sequence may contain an open reading frame or a fragment of an open reading frame. In some embodiments the heterologous object sequence has a Kozak sequence. In some embodiments the heterologous object sequence has an internal ribosome entry site. In some embodiments the heterologous object sequence has a self-cleaving peptide such as a T2A or P2A site. In some embodiments the heterologous object sequence has a start codon. In some embodiments the template RNA has a splice acceptor site. In some embodiments the template RNA has a splice donor site. Exemplary splice acceptor and splice donor sites are described in WO2016044416, incorporated herein by reference in its entirety. Exemplary splice acceptor site sequences are known to those of skill in the art. In some embodiments the template RNA has a microRNA binding site downstream of the stop codon. In some embodiments the template RNA has a polyA tail downstream of the stop codon of an open reading frame. In some embodiments the template RNA comprises one or more exons. In some embodiments the template RNA comprises one or more introns. In some embodiments the template RNA comprises a eukaryotic transcriptional terminator. In some embodiments the template RNA comprises an enhanced translation element or a translation enhancing element. In some embodiments the RNA comprises the human T-cell leukemia virus (HTLV-1) R region. In some embodiments the RNA comprises a posttranscriptional regulatory element that enhances nuclear export, such as that of Hepatitis B Virus (HPRE) or Woodchuck Hepatitis Virus (WPRE).

In some embodiments, the heterologous object sequence may contain a non-coding sequence. For example, the template nucleic acid (e.g., template RNA) may comprise a regulatory element, e.g., a promoter or enhancer sequence or miRNA binding site. In some embodiments, integration of the object sequence at a target site will result in upregulation of an endogenous gene. In some embodiments, integration of the object sequence at a target site will result in downregulation of an endogenous gene. In some embodiments the template nucleic acid (e.g., template RNA) comprises a tissue specific promoter or enhancer, each of which may be unidirectional or bidirectional. In some embodiments the promoter is an RNA polymerase I promoter, RNA polymerase II promoter, or RNA polymerase III promoter. In some embodiments the promoter comprises a TATA element. In some embodiments the promoter comprises a B recognition element. In some embodiments the promoter has one or more binding sites for transcription factors.

In some embodiments, the template nucleic acid (e.g., template RNA) comprises a site that coordinates epigenetic modification. In some embodiments, the template nucleic acid (e.g., template RNA) comprises a chromatin insulator. For example, the template nucleic acid (e.g., template RNA) comprises a CTCF site or a site targeted for DNA methylation.

In some embodiments, the template nucleic acid (e.g., template RNA) comprises a gene expression unit composed of at least one regulatory region operably linked to an effector sequence. The effector sequence may be a sequence that is transcribed into RNA (e.g., a coding sequence or a non-coding sequence such as a sequence encoding a micro RNA).

In some embodiments, the heterologous object sequence of the template nucleic acid (e.g., template RNA) is inserted into a target genome in an endogenous intron. In some embodiments, the heterologous object sequence of the template nucleic acid (e.g., template RNA) is inserted into a target genome and thereby acts as a new exon. In some embodiments, the insertion of the heterologous object sequence into the target genome results in replacement of a natural exon or the skipping of a natural exon.

In some embodiments, the heterologous object sequence of the template nucleic acid (e.g., template RNA) is inserted into the target genome in a genomic safe harbor site, such as AAVS1, CCR5, ROSA26, or albumin locus. In some embodiments, a gene modifying is used to integrate a CAR into the T-cell receptor α constant (TRAC) locus (Eyquem et al Nature 543, 113-117 (2017)). In some embodiments, a gene modifying system is used to integrate a CAR into a T-cell receptor R constant (TRBC) locus. Many other safe harbors have been identified by computational approaches (Pellenz et al Hum Gen Ther 30, 814-828 (2019)) and could be used for gene modifying system-mediated integration. In some embodiments, the heterologous object sequence of the template nucleic acid (e.g., template RNA) is added to the genome in an intergenic or intragenic region. In some embodiments, the heterologous object sequence of the template nucleic acid (e.g., template RNA) is added to the genome 5′ or 3′ within 0.1 kb, 0.25 kb, 0.5 kb, 0.75, kb, 1 kb, 2 kb, 3 kb, 4 kb, 5 kb, 7.5 kb, 10 kb, 15 kb, 20 kb, 25 kb, 50, 75 kb, or 100 kb of an endogenous active gene. In some embodiments, the heterologous object sequence of the template nucleic acid (e.g., template RNA) is added to the genome 5′ or 3′ within 0.1 kb, 0.25 kb, 0.5 kb, 0.75, kb, 1 kb, 2 kb, 3 kb, 4 kb, 5 kb, 7.5 kb, 10 kb, 15 kb, 20 kb, 25 kb, 50, 75 kb, or 100 kb of an endogenous promoter or enhancer. In some embodiments, the heterologous object sequence of the template nucleic acid (e.g., template RNA) can be, e.g., 50-50,000 base pairs (e.g., between 50-40,000 bp, between 500-30,000 bp between 500-20,000 bp, between 100-15,000 bp, between 500-10,000 bp, between 50-10,000 bp, between 50-5,000 bp.

The template nucleic acid (e.g., template RNA) can be designed to result in insertions, mutations, or deletions at the target DNA locus. In some embodiments, the template nucleic acid (e.g., template RNA) may be designed to cause an insertion in the target DNA. For example, the template nucleic acid (e.g., template RNA) may contain a heterologous object sequence, wherein the reverse transcription will result in insertion of the heterologous object sequence into the target DNA. In other embodiments, the RNA template may be designed to write a deletion into the target DNA. For example, the template nucleic acid (e.g., template RNA) may match the target DNA upstream and downstream of the desired deletion, wherein the reverse transcription will result in the copying of the upstream and downstream sequences from the template nucleic acid (e.g., template RNA) without the intervening sequence, e.g., causing deletion of the intervening sequence. In other embodiments, the template nucleic acid (e.g., template RNA) may be designed to write an edit into the target DNA. For example, the template RNA may match the target DNA sequence with the exception of one or more nucleotides, wherein the reverse transcription will result in the copying of these edits into the target DNA, e.g., resulting in mutations, e.g., transition or transversion mutations.

In some embodiments, the pre-edit homology domain comprises a nucleic acid sequence having 100% sequence identity with a nucleic acid sequence comprised in a target nucleic acid molecule.

In some embodiments, the post-edit homology domain comprises a nucleic acid sequence having 100% sequence identity with a nucleic acid sequence comprised in a target nucleic acid molecule.

PBS Sequence

In some embodiments, a template nucleic acid (e.g., template RNA) comprises a PBS sequence. In some embodiments, a PBS sequence is disposed 3′ of the heterologous object sequence and is complementary to a sequence adjacent to a site to be modified by a system described herein, or comprises no more than 1, 2, 3, 4, or 5 mismatches to a sequence complementary to the sequence adjacent to a site to be modified by the system/gene modifying polypeptide. In some embodiments, the PBS sequence binds within 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleotides of a nick site in the target nucleic acid molecule. In some embodiments, binding of the PBS sequence to the target nucleic acid molecule permits initiation of target-primed reverse transcription (TPRT), e.g., with the 3′ homology domain acting as a primer for TPRT. In some embodiments, the PBS sequence is 3-5, 5-10, 10-30, 10-25, 10-20, 10-19, 10-18, 10-17, 10-16, 10-15, 10-14, 10-13, 10-12, 10-11, 11-30, 11-25, 11-20, 11-19, 11-18, 11-17, 11-16, 11-15, 11-14, 11-13, 11-12, 12-30, 12-25, 12-20, 12-19, 12-18, 12-17, 12-16, 12-15, 12-14, 12-13, 13-30, 13-25, 13-20, 13-19, 13-18, 13-17, 13-16, 13-15, 13-14, 14-30, 14-25, 14-20, 14-19, 14-18, 14-17, 14-16, 14-15, 15-30, 15-25, 15-20, 15-19, 15-18, 15-17, 15-16, 16-30, 16-25, 16-20, 16-19, 16-18, 16-17, 17-30, 17-25, 17-20, 17-19, 17-18, 18-30, 18-25, 18-20, 18-19, 19-30, 19-25, 19-20, 20-30, 20-25, or 25-30 nucleotides in length, e.g., 10-17, 12-16, or 12-14 nucleotides in length. In some embodiments, the PBS sequence is 5-20, 8-16, 8-14, 8-13, 9-13, 9-12, or 10-12 nucleotides in length, e.g., 9-12 nucleotides in length.

The template nucleic acid (e.g., template RNA) may have some homology to the target DNA. In some embodiments, the template nucleic acid (e.g., template RNA) PBS sequence domain may serve as an annealing region to the target DNA, such that the target DNA is positioned to prime the reverse transcription of the template nucleic acid (e.g., template RNA). In some embodiments the template nucleic acid (e.g., template RNA) has at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 175, 200 or more bases of exact homology to the target DNA at the 3′ end of the RNA. In some embodiments the template nucleic acid (e.g., template RNA) has at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 175, 200 or more bases of at least 50%, 60%, 70%, 80%, 85%, 90%, 95%, 97%, 98%, 99% or 100% homology to the target DNA, e.g., at the 5′ end of the template nucleic acid (e.g., template RNA).

gRNAs with Inducible Activity

In some embodiments, a gRNA described herein (e.g., a gRNA that is part of a template RNA or a gRNA used for second strand nicking) has inducible activity. Inducible activity may be achieved by the template nucleic acid, e.g., template RNA, further comprising (in addition to the gRNA) a blocking domain, wherein the sequence of a portion of or all of the blocking domain is at least partially complementary to a portion or all of the gRNA. The blocking domain is thus capable of hybridizing or substantially hybridizing to a portion of or all of the gRNA. In some embodiments, the blocking domain and inducibly active gRNA are disposed on the template nucleic acid, e.g., template RNA, such that the gRNA can adopt a first conformation where the blocking domain is hybridized or substantially hybridized to the gRNA, and a second conformation where the blocking domain is not hybridized or not substantially hybridized to the gRNA. In some embodiments, in the first conformation the gRNA is unable to bind to the gene modifying polypeptide (e.g., the template nucleic acid binding domain, DNA binding domain, or endonuclease domain (e.g., a CRISPR/Cas protein)) or binds with substantially decreased affinity compared to an otherwise similar template RNA lacking the blocking domain. In some embodiments, in the second conformation the gRNA is able to bind to the gene modifying polypeptide (e.g., the template nucleic acid binding domain, DNA binding domain, or endonuclease domain (e.g., a CRISPR/Cas protein)). In some embodiments, whether the gRNA is in the first or second conformation can influence whether the DNA binding or endonuclease activities of the gene modifying polypeptide (e.g., of the CRISPR/Cas protein the gene modifying polypeptide comprises) are active.

In some embodiments, the gRNA that coordinates the second nick has inducible activity. In some embodiments, the gRNA that coordinates the second nick is induced after the template is reverse transcribed. In some embodiments, hybridization of the gRNA to the blocking domain can be disrupted using an opener molecule. In some embodiments, an opener molecule comprises an agent that binds to a portion or all of the gRNA or blocking domain and inhibits hybridization of the gRNA to the blocking domain. In some embodiments, the opener molecule comprises a nucleic acid, e.g., comprising a sequence that is partially or wholly complementary to the gRNA, blocking domain, or both. By choosing or designing an appropriate opener molecule, providing the opener molecule can promote a change in the conformation of the gRNA such that it can associate with a CRISPR/Cas protein and provide the associated functions of the CRISPR/Cas protein (e.g., DNA binding and/or endonuclease activity). Without wishing to be bound by theory, providing the opener molecule at a selected time and/or location may allow for spatial and temporal control of the activity of the gRNA, CRISPR/Cas protein, or gene modifying system comprising the same. In some embodiments, the opener molecule is exogenous to the cell comprising the gene modifying polypeptide and or template nucleic acid. In some embodiments, the opener molecule comprises an endogenous agent (e.g., endogenous to the cell comprising the gene modifying polypeptide and or template nucleic acid comprising the gRNA and blocking domain). For example, an inducible gRNA, blocking domain, and opener molecule may be chosen such that the opener molecule is an endogenous agent expressed in a target cell or tissue, e.g., thereby ensuring activity of a gene modifying system in the target cell or tissue. As a further example, an inducible gRNA, blocking domain, and opener molecule may be chosen such that the opener molecule is absent or not substantially expressed in one or more non-target cells or tissues, e.g., thereby ensuring that activity of a gene modifying system does not occur or substantially occur in the one or more non-target cells or tissues, or occurs at a reduced level compared to a target cell or tissue. Exemplary blocking domains, opener molecules, and uses thereof are described in PCT App. Publication WO2020044039A1, which is incorporated herein by reference in its entirety. In some embodiments, the template nucleic acid, e.g., template RNA, may comprise one or more sequences or structures for binding by one or more components of a gene modifying polypeptide, e.g., by a reverse transcriptase or RNA binding domain, and a gRNA. In some embodiments, the gRNA facilitates interaction with the template nucleic acid binding domain (e.g., RNA binding domain) of the gene modifying polypeptide. In some embodiments, the gRNA directs the gene modifying polypeptide to the matching target sequence, e.g., in a target cell genome.

Circular RNAs and Ribozymes in Gene Modifying Systems

It is contemplated that it may be useful to employ circular and/or linear RNA states during the formulation, delivery, or gene modifying reaction within the target cell. Thus, in some embodiments of any of the aspects described herein, a gene modifying system comprises one or more circular RNAs (circRNAs). In some embodiments of any of the aspects described herein, a gene modifying system comprises one or more linear RNAs. In some embodiments, a nucleic acid as described herein (e.g., a template nucleic acid, a nucleic acid molecule encoding a gene modifying polypeptide, or both) is a circRNA. In some embodiments, a circular RNA molecule encodes the gene modifying polypeptide. In some embodiments, the circRNA molecule encoding the gene modifying polypeptide is delivered to a host cell. In some embodiments, a circular RNA molecule encodes a recombinase, e.g., as described herein. In some embodiments, the circRNA molecule encoding the recombinase is delivered to a host cell. In some embodiments, the circRNA molecule encoding the gene modifying polypeptide is linearized (e.g., in the host cell, e.g., in the nucleus of the host cell) prior to translation.

Circular RNAs (circRNAs) have been found to occur naturally in cells and have been found to have diverse functions, including both non-coding and protein coding roles in human cells. It has been shown that a circRNA can be engineered by incorporating a self-splicing intron into an RNA molecule (or DNA encoding the RNA molecule) that results in circularization of the RNA, and that an engineered circRNA can have enhanced protein production and stability (Wesselhoeft et al. Nature Communications 2018). In some embodiments, the gene modifying polypeptide is encoded as circRNA. In certain embodiments, the template nucleic acid is a DNA, such as a dsDNA or ssDNA. In certain embodiments, the circDNA comprises a template RNA.

In some embodiments, the circRNA comprises one or more ribozyme sequences. In some embodiments, the ribozyme sequence is activated for autocleavage, e.g., in a host cell, e.g., thereby resulting in linearization of the circRNA. In some embodiments, the ribozyme is activated when the concentration of magnesium reaches a sufficient level for cleavage, e.g., in a host cell. In some embodiments the circRNA is maintained in a low magnesium environment prior to delivery to the host cell. In some embodiments, the ribozyme is a protein-responsive ribozyme. In some embodiments, the ribozyme is a nucleic acid-responsive ribozyme. In some embodiments, the circRNA comprises a cleavage site. In some embodiments, the circRNA comprises a second cleavage site.

In some embodiments, the circRNA is linearized in the nucleus of a target cell. In some embodiments, linearization of a circRNA in the nucleus of a cell involves components present in the nucleus of the cell, e.g., to activate a cleavage event. In some embodiments, a ribozyme, e.g., a ribozyme from a B2 or ALU element, that is responsive to a nuclear element, e.g., a nuclear protein, e.g., a genome-interacting protein, e.g., an epigenetic modifier, e.g., EZH2, is incorporated into a circRNA, e.g., of a gene modifying system. In some embodiments, nuclear localization of the circRNA results in an increase in autocatalytic activity of the ribozyme and linearization of the circRNA.

In some embodiments, the ribozyme is heterologous to one or more of the other components of the gene modifying system. In some embodiments, an inducible ribozyme (e.g., in a circRNA as described herein) is created synthetically, for example, by utilizing a protein ligand-responsive aptamer design. A system for utilizing the satellite RNA of tobacco ringspot virus hammerhead ribozyme with an MS2 coat protein aptamer has been described (Kennedy et al. Nucleic Acids Res 42(19):12306-12321 (2014), incorporated herein by reference in its entirety) that results in activation of the ribozyme activity in the presence of the MS2 coat protein. In embodiments, such a system responds to protein ligand localized to the cytoplasm or the nucleus. In some embodiments the protein ligand is not MS2. Methods for generating RNA aptamers to target ligands have been described, for example, based on the systematic evolution of ligands by exponential enrichment (SELEX) (Tuerk and Gold, Science 249(4968):505-510 (1990); Ellington and Szostak, Nature 346(6287):818-822 (1990); the methods of each of which are incorporated herein by reference) and have, in some instances, been aided by in silico design (Bell et al. PNAS 117(15):8486-8493, the methods of which are incorporated herein by reference). Thus, in some embodiments, an aptamer for a target ligand is generated and incorporated into a synthetic ribozyme system, e.g., to trigger ribozyme-mediated cleavage and circRNA linearization, e.g., in the presence of the protein ligand. In some embodiments, circRNA linearization is triggered in the cytoplasm, e.g., using an aptamer that associates with a ligand in the cytoplasm. In some embodiments, circRNA linearization is triggered in the nucleus, e.g., using an aptamer that associates with a ligand in the nucleus. In embodiments, the ligand in the nucleus comprises an epigenetic modifier or a transcription factor. In some embodiments the ligand that triggers linearization is present at higher levels in on-target cells than off-target cells.

It is further contemplated that a nucleic acid-responsive ribozyme system can be employed for circRNA linearization. For example, biosensors that sense defined target nucleic acid molecules to trigger ribozyme activation are described, e.g., in Penchovsky (Biotechnology Advances 32(5):1015-1027 (2014), incorporated herein by reference). By these methods, a ribozyme naturally folds into an inactive state and is only activated in the presence of a defined target nucleic acid molecule (e.g., an RNA molecule). In some embodiments, a circRNA of a gene modifying system comprises a nucleic acid-responsive ribozyme that is activated in the presence of a defined target nucleic acid, e.g., an RNA, e.g., an mRNA, miRNA, guide RNA, gRNA, sgRNA, ncRNA, lncRNA, tRNA, snRNA, or mtRNA. In some embodiments the nucleic acid that triggers linearization is present at higher levels in on-target cells than off-target cells.

In some embodiments of any of the aspects herein, a gene modifying system incorporates one or more ribozymes with inducible specificity to a target tissue or target cell of interest, e.g., a ribozyme that is activated by a ligand or nucleic acid present at higher levels in a target tissue or target cell of interest. In some embodiments, the gene modifying system incorporates a ribozyme with inducible specificity to a subcellular compartment, e.g., the nucleus, nucleolus, cytoplasm, or mitochondria. In some embodiments, the ribozyme that is activated by a ligand or nucleic acid present at higher levels in the target subcellular compartment. In some embodiments, an RNA component of a gene modifying system is provided as circRNA, e.g., that is activated by linearization. In some embodiments, linearization of a circRNA encoding a gene modifying polypeptide activates the molecule for translation. In some embodiments, a signal that activates a circRNA component of a gene modifying system is present at higher levels in on-target cells or tissues, e.g., such that the system is specifically activated in these cells.

In some embodiments, an RNA component of a gene modifying system is provided as a circRNA that is inactivated by linearization. In some embodiments, a circRNA encoding the gene modifying polypeptide is inactivated by cleavage and degradation. In some embodiments, a circRNA encoding the gene modifying polypeptide is inactivated by cleavage that separates a translation signal from the coding sequence of the polypeptide. In some embodiments, a signal that inactivates a circRNA component of a gene modifying system is present at higher levels in off-target cells or tissues, such that the system is specifically inactivated in these cells.

Target Nucleic Acid Site

In some embodiments, after gene modification, the target site surrounding the edited sequence contains a limited number of insertions or deletions, for example, in less than about 50% or 10% of editing events, e.g., as determined by long-read amplicon sequencing of the target site, e.g., as described in Karst et al. (2020) bioRxiv doi.org/10.1101/645903 (incorporated by reference herein in its entirety). In some embodiments, the target site does not show multiple consecutive editing events, e.g., head-to-tail or head-to-head duplications, e.g., as determined by long-read amplicon sequencing of the target site, e.g., as described in Karst et al. bioRxiv doi.org/10.1101/645903 (2020) (incorporated herein by reference in its entirety). In some embodiments, the target site contains an integrated sequence corresponding to the template RNA. In some embodiments, the target site does not contain insertions resulting from endogenous RNA in more than about 1% or 10% of events, e.g., as determined by long-read amplicon sequencing of the target site, e.g., as described in Karst et al. bioRxiv doi.org/10.1101/645903 (2020) (incorporated herein by reference in its entirety). In some embodiments, the target site contains the integrated sequence corresponding to the template RNA.

In certain aspects of the present invention, the host DNA-binding site integrated into by the gene modifying system can be in a gene, in an intron, in an exon, an ORF, outside of a coding region of any gene, in a regulatory region of a gene, or outside of a regulatory region of a gene. In other aspects, the polypeptide may bind to one or more than one host DNA sequence.

In some embodiments, a gene modifying system is used to edit a target locus in multiple alleles. In some embodiments, a gene modifying system is designed to edit a specific allele. For example, a gene modifying polypeptide may be directed to a specific sequence that is only present on one allele, e.g., comprises a template RNA with homology to a target allele, e.g., a gRNA or annealing domain, but not to a second cognate allele. In some embodiments, a gene modifying system can alter a haplotype-specific allele. In some embodiments, a gene modifying system that targets a specific allele preferentially targets that allele, e.g., has at least a 2, 4, 6, 8, or 10-fold preference for a target allele.

Second Strand Nicking

In some embodiments, a gene modifying system described herein comprises a nickase activity (e.g., in the gene modifying polypeptide) that nicks the first strand, and a nickase activity (e.g., in a polypeptide separate from the gene modifying polypeptide) that nicks the second strand of target DNA. As discussed herein, without wishing to be bound by theory, nicking of the first strand of the target site DNA is thought to provide a 3′ OH that can be used by an RT domain to reverse transcribe a sequence of a template RNA, e.g., a heterologous object sequence. Without wishing to be bound by theory, it is thought that introducing an additional nick to the second strand may bias the cellular DNA repair machinery to adopt the heterologous object sequence-based sequence more frequently than the original genomic sequence. In some embodiments, the additional nick to the second strand is made by the same endonuclease domain (e.g., nickase domain) as the nick to the first strand. In some embodiments, the same gene modifying polypeptide performs both the nick to the first strand and the nick to the second strand. In some embodiments, the gene modifying polypeptide comprises a CRISPR/Cas domain and the additional nick to the second strand is directed by an additional nucleic acid, e.g., comprising a second gRNA directing the CRISPR/Cas domain to nick the second strand. In other embodiments, the additional second strand nick is made by a different endonuclease domain (e.g., nickase domain) than the nick to the first strand. In some embodiments, that different endonuclease domain is situated in an additional polypeptide (e.g., a system of the invention further comprises the additional polypeptide), separate from the gene modifying polypeptide. In some embodiments, the additional polypeptide comprises an endonuclease domain (e.g., nickase domain) described herein. In some embodiments, the additional polypeptide comprises a DNA binding domain, e.g., described herein.

It is contemplated herein that the position at which the second strand nick occurs relative to the first strand nick may influence the extent to which one or more of: desired gene modifying DNA modifications are obtained, undesired double-strand breaks (DSBs) occur, undesired insertions occur, or undesired deletions occur. Without wishing to be bound by theory, second strand nicking may occur in two general orientations: inward nicks and outward nicks.

In some embodiments, in the inward nick orientation, the RT domain polymerizes (e.g., using the template RNA (e.g., the heterologous object sequence)) away from the second strand nick. In some embodiments, in the inward nick orientation, the location of the nick to the first strand and the location of the nick to the second strand are positioned between the first PAM site and second PAM site (e.g., in a scenario wherein both nicks are made by a polypeptide (e.g., a gene modifying polypeptide) comprising a CRISPR/Cas domain). When there are two PAMs on the outside and two nicks on the inside, this inward nick orientation can also be referred to as “PAM-out”. In some embodiments, in the inward nick orientation, the location of the nick to the first strand and the location of the nick to the second strand are between the sites where the polypeptide and the additional polypeptide bind to the target DNA. In some embodiments, in the inward nick orientation, the location of the nick to the second strand is positioned between the binding sites of the polypeptide and additional polypeptide, and the nick to the first strand is also located between the binding sites of the polypeptide and additional polypeptide. In some embodiments, in the inward nick orientation, the location of the nick to the first strand and the location of the nick to the second strand are positioned between the PAM site and the binding site of the second polypeptide which is at a distance from the target site.

An example of a gene modifying system that provides an inward nick orientation comprises a gene modifying polypeptide comprising a CRISPR/Cas domain, a template RNA comprising a gRNA that directs nicking of the target site DNA on the first strand, and an additional nucleic acid comprising an additional gRNA that directs nicking at a site a distance from the location of the first nick, wherein the location of the first nick and the location of the second nick are between the PAM sites of the sites to which the two gRNAs direct the gene modifying polypeptide. As a further example, another gene modifying system that provides an inward nick orientation comprises a gene modifying polypeptide comprising a zinc finger molecule and a first nickase domain wherein the zinc finger molecule binds to the target DNA in a manner that directs the first nickase domain to nick the first strand of the target site; an additional polypeptide comprising a CRISPR/Cas domain, and an additional nucleic acid comprising a gRNA that directs the additional polypeptide to nick a site a distance from the target site DNA on the second strand, wherein the location of the first nick and the location of the second nick are between the PAM site and the site to which the zinc finger molecule binds. As a further example, another gene modifying system that provides an inward nick orientation comprises a gene modifying polypeptide comprising a zinc finger molecule and a first nickase domain wherein the zinc finger molecule binds to the target DNA in a manner that directs the first nickase domain to nick the first strand of the target site; an additional polypeptide comprising a TAL effector molecule and a second nickase domain wherein the TAL effector molecule binds to a site a distance from the target site in a manner that directs the additional polypeptide to nick the second strand, wherein the location of the first nick and the location of the second nick are between the site to which the TAL effector molecule binds and the site to which the zinc finger molecule binds.

In some embodiments, in the outward nick orientation, the RT domain polymerizes (e.g., using the template RNA (e.g., the heterologous object sequence)) toward the second strand nick. In some embodiments, in the outward nick orientation when both the first and second nicks are made by a polypeptide comprising a CRISPR/Cas domain (e.g., a gene modifying polypeptide), the first PAM site and second PAM site are positioned between the location of the nick to the first strand and the location of the nick to the second strand. When there are two PAMs on the inside and two nicks on the outside, this outward nick orientation also can be referred to as “PAM-in”. In some embodiments, in the outward nick orientation, the polypeptide (e.g., the gene modifying polypeptide) and the additional polypeptide bind to sites on the target DNA between the location of the nick to the first strand and the location of the nick to the second. In some embodiments, in the outward nick orientation, the location of the nick to the second strand is positioned on the opposite side of the binding sites of the polypeptide and additional polypeptide relative to the location of the nick to the first strand. In some embodiments, in the outward orientation, the PAM site and the binding site of the second polypeptide which is at a distance from the target site are positioned between the location of the nick to the first strand and the location of the nick to the second strand.

An example of a gene modifying system that provides an outward nick orientation comprises a gene modifying polypeptide comprising a CRISPR/Cas domain, a template RNA comprising a gRNA that directs nicking of the target site DNA on the first strand, and an additional nucleic acid comprising an additional gRNA that directs nicking at a site a distance from the location of the first nick, wherein the location of the first nick and the location of the second nick are outside of the PAM sites of the sites to which the two gRNAs direct the gene modifying polypeptide (i.e., the PAM sites are between the location of the first nick and the location of the second nick). As a further example, another gene modifying system that provides an outward nick orientation comprises a gene modifying polypeptide comprising a zinc finger molecule and a first nickase domain wherein the zinc finger molecule binds to the target DNA in a manner that directs the first nickase domain to nick the first strand of the target site; an additional polypeptide comprising a CRISPR/Cas domain, and an additional nucleic acid comprising a gRNA that directs the additional polypeptide to nick a site a distance from the target site DNA on the second strand, wherein the location of the first nick and the location of the second nick are outside the PAM site and the site to which the zinc finger molecule binds (i.e., the PAM site and the site to which the zinc finger molecule binds are between the location of the first nick and the location of the second nick). As a further example, another gene modifying system that provides an outward nick orientation comprises a gene modifying polypeptide comprising a zinc finger molecule and a first nickase domain wherein the zinc finger molecule binds to the target DNA in a manner that directs the first nickase domain to nick the first strand of the target site; an additional polypeptide comprising a TAL effector molecule and a second nickase domain wherein the TAL effector molecule binds to a site a distance from the target site in a manner that directs the additional polypeptide to nick the second strand, wherein the location of the first nick and the location of the second nick are outside the site to which the TAL effector molecule binds and the site to which the zinc finger molecule binds (i.e., the site to which the TAL effector molecule binds and the site to which the zinc finger molecule binds are between the location of the first nick and the location of the second nick).

Without wishing to be bound by theory, it is thought that, for gene modifying systems where a second strand nick is provided, an outward nick orientation is preferred in some embodiments. As is described herein, an inward nick may produce a higher number of double-strand breaks (DSBs) than an outward nick orientation. DSBs may be recognized by the DSB repair pathways in the nucleus of a cell, which can result in undesired insertions and deletions. An outward nick orientation may provide a decreased risk of DSB formation, and a corresponding lower amount of undesired insertions and deletions. In some embodiments, undesired insertions and deletions are insertions and deletions not encoded by the heterologous object sequence, e.g., an insertion or deletion produced by the double-strand break repair pathway unrelated to the modification encoded by the heterologous object sequence. In some embodiments, a desired gene modification comprises a change to the target DNA (e.g., a substitution, insertion, or deletion) encoded by the heterologous object sequence (e.g., and achieved by the gene modifying writing the heterologous object sequence into the target site). In some embodiments, the first strand nick and the second strand nick are in an outward orientation.

In addition, the distance between the first strand nick and second strand nick may influence the extent to which one or more of: desired gene modifying system DNA modifications are obtained, undesired double-strand breaks (DSBs) occur, undesired insertions occur, or undesired deletions occur. Without wishing to be bound by theory, it is thought the second strand nick benefit, the biasing of DNA repair toward incorporation of the heterologous object sequence into the target DNA, increases as the distance between the first strand nick and second strand nick decreases. However, it is thought that the risk of DSB formation also increases as the distance between the first strand nick and second strand nick decreases. Correspondingly, it is thought that the number of undesired insertions and/or deletions may increase as the distance between the first strand nick and second strand nick decreases. In some embodiments, the distance between the first strand nick and second strand nick is chosen to balance the benefit of biasing DNA repair toward incorporation of the heterologous object sequence into the target DNA and the risk of DSB formation and of undesired deletions and/or insertions. In some embodiments, a system where the first strand nick and the second strand nick are at least a threshold distance apart has an increased level of desired gene modifying system modification outcomes, a decreased level of undesired deletions, and/or a decreased level of undesired insertions relative to an otherwise similar inward nick orientation system where the first nick and the second nick are less than the a threshold distance apart. In some embodiments the threshold distance(s) is given below.

In some embodiments, the first nick and the second nick are at least 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, or 200 nucleotides apart. In some embodiments, the first nick and the second nick are no more than 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, or 250 nucleotides apart. In some embodiments, the first nick and the second nick are 20-200, 30-200, 40-200, 50-200, 60-200, 70-200, 80-200, 90-200, 100-200, 110-200, 120-200, 130-200, 140-200, 150-200, 160-200, 170-200, 180-200, 190-200, 20-190, 30-190, 40-190, 50-190, 60-190, 70-190, 80-190, 90-190, 100-190, 110-190, 120-190, 130-190, 140-190, 150-190, 160-190, 170-190, 180-190, 20-180, 30-180, 40-180, 50-180, 60-180, 70-180, 80-180, 90-180, 100-180, 110-180, 120-180, 130-180, 140-180, 150-180, 160-180, 170-180, 20-170, 30-170, 40-170, 50-170, 60-170, 70-170, 80-170, 90-170, 100-170, 110-170, 120-170, 130-170, 140-170, 150-170, 160-170, 20-160, 30-160, 40-160, 50-160, 60-160, 70-160, 80-160, 90-160, 100-160, 110-160, 120-160, 130-160, 140-160, 150-160, 20-150, 30-150, 40-150, 50-150, 60-150, 70-150, 80-150, 90-150, 100-150, 110-150, 120-150, 130-150, 140-150, 20-140, 30-140, 40-140, 50-140, 60-140, 70-140, 80-140, 90-140, 100-140, 110-140, 120-140, 130-140, 20-130, 30-130, 40-130, 50-130, 60-130, 70-130, 80-130, 90-130, 100-130, 110-130, 120-130, 20-120, 30-120, 40-120, 50-120, 60-120, 70-120, 80-120, 90-120, 100-120, 110-120, 20-110, 30-110, 40-110, 50-110, 60-110, 70-110, 80-110, 90-110, 100-110, 20-100, 30-100, 40-100, 50-100, 60-100, 70-100, 80-100, 90-100, 20-90, 30-90, 40-90, 50-90, 60-90, 70-90, 80-90, 20-80, 30-80, 40-80, 50-80, 60-80, 70-80, 20-70, 30-70, 40-70, 50-70, 60-70, 20-60, 30-60, 40-60, 50-60, 20-50, 30-50, 40-50, 20-40, 30-40, or 20-30 nucleotides apart. In some embodiments, the first nick and the second nick are 40-100 nucleotides apart.

Without wishing to be bound by theory, it is thought that, for gene modifying systems where a second strand nick is provided and an inward nick orientation is selected, increasing the distance between the first strand nick and second strand nick may be preferred. As is described herein, an inward nick orientation may produce a higher number of DSBs than an outward nick orientation, and may result in a higher amount of undesired insertions and deletions than an outward nick orientation, but increasing the distance between the nicks may mitigate that increase in DSBs, undesired deletions, and/or undesired insertions. In some embodiments, an inward nick orientation wherein the first nick and the second nick are at least a threshold distance apart has an increased level of desired gene modifying system modification outcomes, a decreased level of undesired deletions, and/or a decreased level of undesired insertions relative to an otherwise similar inward nick orientation system where the first nick and the second nick are less than the threshold distance apart. In some embodiments the threshold distance is given below.

In some embodiments, the first strand nick and the second strand nick are in an inward orientation. In some embodiments, the first strand nick and the second strand nick are in an inward orientation and the first strand nick and second strand nick are at least 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 220, 240, 260, 280, 300, 350, 400, 450, or 500 nucleotides apart, e.g., at least 100 nucleotides apart, (and optionally no more than 500, 400, 300, 200, 190, 180, 170, 160, 150, 140, 130, or 120 nucleotides apart). In some embodiments, the first strand nick and the second strand nick are in an inward orientation and the first strand nick and second strand nick are 100-200, 110-200, 120-200, 130-200, 140-200, 150-200, 160-200, 170-200, 180-200, 190-200, 100-190, 110-190, 120-190, 130-190, 140-190, 150-190, 160-190, 170-190, 180-190, 100-180, 110-180, 120-180, 130-180, 140-180, 150-180, 160-180, 170-180, 100-170, 110-170, 120-170, 130-170, 140-170, 150-170, 160-170, 100-160, 110-160, 120-160, 130-160, 140-160, 150-160, 100-150, 110-150, 120-150, 130-150, 140-150, 100-140, 110-140, 120-140, 130-140, 100-130, 110-130, 120-130, 100-120, 110-120, or 100-110 nucleotides apart.

Chemically Modified Nucleic Acids and Nucleic Acid End Features

A nucleic acid described herein (e.g., a template nucleic acid, e.g., a template RNA; or a nucleic acid (e.g., mRNA) encoding a gene modifying polypeptide; or a gRNA) can comprise unmodified or modified nucleobases. Naturally occurring RNAs are synthesized from four basic ribonucleotides: ATP, CTP, UTP and GTP, but may contain post-transcriptionally modified nucleotides. Further, approximately one hundred different nucleoside modifications have been identified in RNA (Rozenski, J, Crain, P, and McCloskey, J. (1999). The RNA Modification Database: 1999 update. Nucl Acids Res 27: 196-197). An RNA can also comprise wholly synthetic nucleotides that do not occur in nature.

In some embodiments, the chemical modification is one provided in WO/2016/183482, US Pat. Pub. No. 20090286852, of International Application No. WO/2012/019168, WO/2012/045075, WO/2012/135805, WO/2012/158736, WO/2013/039857, WO/2013/039861, WO/2013/052523, WO/2013/090648, WO/2013/096709, WO/2013/101690, WO/2013/106496, WO/2013/130161, WO/2013/151669, WO/2013/151736, WO/2013/151672, WO/2013/151664, WO/2013/151665, WO/2013/151668, WO/2013/151671, WO/2013/151667, WO/2013/151670, WO/2013/151666, WO/2013/151663, WO/2014/028429, WO/2014/081507, WO/2014/093924, WO/2014/093574, WO/2014/113089, WO/2014/144711, WO/2014/144767, WO/2014/144039, WO/2014/152540, WO/2014/152030, WO/2014/152031, WO/2014/152027, WO/2014/152211, WO/2014/158795, WO/2014/159813, WO/2014/164253, WO/2015/006747, WO/2015/034928, WO/2015/034925, WO/2015/038892, WO/2015/048744, WO/2015/051214, WO/2015/051173, WO/2015/051169, WO/2015/058069, WO/2015/085318, WO/2015/089511, WO/2015/105926, WO/2015/164674, WO/2015/196130, WO/2015/196128, WO/2015/196118, WO/2016/011226, WO/2016/011222, WO/2016/011306, WO/2016/014846, WO/2016/022914, WO/2016/036902, WO/2016/077125, or WO/2016/077123, each of which is herein incorporated by reference in its entirety. It is understood that incorporation of a chemically modified nucleotide into a polynucleotide can result in the modification being incorporated into a nucleobase, the backbone, or both, depending on the location of the modification in the nucleotide. In some embodiments, the backbone modification is one provided in EP 2813570, which is herein incorporated by reference in its entirety. In some embodiments, the modified cap is one provided in US Pat. Pub. No. 20050287539, which is herein incorporated by reference in its entirety.

In some embodiments, the chemically modified nucleic acid (e.g., RNA, e.g., mRNA) comprises one or more of ARCA: anti-reverse cap analog (m27.3′-OGP3G), GP3G (Unmethylated Cap Analog), m7GP3G (Monomethylated Cap Analog), m32.2.7GP3G (Trimethylated Cap Analog), m5CTP (5′-methyl-cytidine triphosphate), m6ATP (N6-methyl-adenosine-5′-triphosphate), s2UTP (2-thio-uridine triphosphate), and Ψ (pseudouridine triphosphate).

In some embodiments, the chemically modified nucleic acid comprises a 5′ cap, e.g.: a 7-methylguanosine cap (e.g., a 0-Me-m7G cap); a hypermethylated cap analog; an NAD+-derived cap analog (e.g., as described in Kiledjian, Trends in Cell Biology 28, 454-464 (2018)); or a modified, e.g., biotinylated, cap analog (e.g., as described in Bednarek et al., Phil Trans R Soc B 373, 20180167 (2018)).

In some embodiments, the chemically modified nucleic acid comprises a 3′ feature selected from one or more of: a polyA tail; a 16-nucleotide long stem-loop structure flanked by unpaired 5 nucleotides (e.g., as described by Mannironi et al., Nucleic Acid Research 17, 9113-9126 (1989)); a triple-helical structure (e.g., as described by Brown et al., PNAS 109, 19202-19207 (2012)); a tRNA, Y RNA, or vault RNA structure (e.g., as described by Labno et al., Biochemica et Biophysica Acta 1863, 3125-3147 (2016)); incorporation of one or more deoxyribonucleotide triphosphates (dNTPs), 2′O-Methylated NTPs, or phosphorothioate-NTPs; a single nucleotide chemical modification (e.g., oxidation of the 3′ terminal ribose to a reactive aldehyde followed by conjugation of the aldehyde-reactive modified nucleotide); or chemical ligation to another nucleic acid molecule.

In some embodiments, the nucleic acid (e.g., template nucleic acid) comprises one or more modified nucleotides, e.g., selected from dihydrouridine, inosine, 7-methylguanosine, 5-methylcytidine (5mC), 5′ Phosphate ribothymidine, 2′-O-methyl ribothymidine, 2′-O-ethyl ribothymidine, 2′-fluoro ribothymidine, C-5 propynyl-deoxycytidine (pdC), C-5 propynyl-deoxyuridine (pdU), C-5 propynyl-cytidine (pC), C-5 propynyl-uridine (pU), 5-methyl cytidine, 5-methyl uridine, 5-methyl deoxycytidine, 5-methyl deoxyuridine methoxy, 2,6-diaminopurine, 5′-Dimethoxytrityl-N4-ethyl-2′-deoxycytidine, C-5 propynyl-f-cytidine (pfC), C-5 propynyl-f-uridine (pfU), 5-methyl f-cytidine, 5-methyl f-uridine, C-5 propynyl-m-cytidine (pmC), C-5 propynyl-f-uridine (pmU), 5-methyl m-cytidine, 5-methyl m-uridine, LNA (locked nucleic acid), MGB (minor groove binder) pseudouridine (Ψ), 1-N-methylpseudouridine (1-Me-Ψ), or 5-methoxyuridine (5-MO-U).

In some embodiments, the nucleic acid comprises a backbone modification, e.g., a modification to a sugar or phosphate group in the backbone. In some embodiments, the nucleic acid comprises a nucleobase modification.

In some embodiments, the nucleic acid comprises one or more chemically modified nucleotides of Table 13, one or more chemical backbone modifications of Table 14, one or more chemically modified caps of Table 15. For instance, in some embodiments, the nucleic acid comprises two or more (e.g., 3, 4, 5, 6, 7, 8, 9, or 10 or more) different types of chemical modifications. As an example, the nucleic acid may comprise two or more (e.g., 3, 4, 5, 6, 7, 8, 9, or 10 or more) different types of modified nucleobases, e.g., as described herein, e.g., in Table 13. Alternatively or in combination, the nucleic acid may comprise two or more (e.g., 3, 4, 5, 6, 7, 8, 9, or 10 or more) different types of backbone modifications, e.g., as described herein, e.g., in Table 14. Alternatively or in combination, the nucleic acid may comprise one or more modified cap, e.g., as described herein, e.g., in Table 15. For instance, in some embodiments, the nucleic acid comprises one or more type of modified nucleobase and one or more type of backbone modification; one or more type of modified nucleobase and one or more modified cap; one or more type of modified cap and one or more type of backbone modification; or one or more type of modified nucleobase, one or more type of backbone modification, and one or more type of modified cap.

In some embodiments, the nucleic acid comprises one or more (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900, 1000, or more) modified nucleobases. In some embodiments, all nucleobases of the nucleic acid are modified. In some embodiments, the nucleic acid is modified at one or more (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900, 1000, or more) positions in the backbone. In some embodiments, all backbone positions of the nucleic acid are modified.

TABLE 13 Modified nucleotides 5-aza-uridine N2-methyl-6-thio-guanosine 2-thio-5-aza-midine N2,N2-dimethyl-6-thio-guanosine 2-thiouridine pyridin-4-one ribonucleoside 4-thio-pseudouridine 2-thio-5-aza-uridine 2-thio-pseudouridine 2-thiomidine 5-hydroxyuridine 4-thio-pseudomidine 3-methyluridine 2-thio-pseudowidine 5-carboxymethyl-uridine 3-methylmidine 1-carboxymethyl-pseudouridine 1-propynyl-pseudomidine 5-propynyl-uridine 1-methyl-1-deaza-pseudomidine 1-propynyl-pseudouridine 2-thio-1-methyl-1-deaza-pseudouridine 5-taurinomethyluridine 4-methoxy-pseudomidine 1-taurinomethyl-pseudouridine 5'-O-(1-Thiophosphate)-Adenosine 5-taurinomethyl-2-thio-uridine 5'-O-(1-Thiophosphate)-Cytidine 1-taurinomethyl-4-thio-uridine 5'-O-(1-thiophosphate)-Guanosine 5-methyl-uridine 5'-O-(1-Thiophophate)-Uridine 1-methyl-pseudouridine 5'-O-(1-Thiophosphate)-Pseudouridine 4-thio-1-methyl-pseudouridine 2'-O-methyl-Adenosine 2-thio-1-methyl-pseudouridine 2'-O-methyl-Cytidine 1-methyl-1-deaza-pseudouridine 2'-O-methyl-Guanosine 2-thio-1-methyl-1-deaza-pseudomidine 2'-O-methyl-Uridine dihydrouridine 2'-O-methyl-Pseudouridine dihydropseudouridine 2'-O-methyl-Inosine 2-thio-dihydromidine 2-methyladenosine 2-thio-dihydropseudouridine 2-methylthio-N6-methyladenosine 2-methoxyuridine 2-methylthio-N6 isopentenyladenosine 2-methoxy-4-thio-uridine 2-methylthio-N6-(cis- 4-methoxy-pseudouridine hydroxyisopentenyl)adenosine 4-methoxy-2-thio-pseudouridine N6-methyl-N6-threonylcarbamoyladenosine 5-aza-cytidine N6-hydroxynorvalylcarbamoyladenosine pseudoisocytidine 3-methyl-cytidine 2-methylthio-N6-hydroxynorvalyl N4-acetylcytidine carbamoyladenosine 5-formylcytidine 2'-O-ribosyladenosine (phosphate) N4-methylcytidine 1,2'-O-dimethylinosine 5-hydroxymethylcytidine 5,2'-O-dimethylcytidine 1-methyl-pseudoisocytidine N4-acetyl-2'-O-methylcytidine pyrrolo-cytidine Lysidine pyrrolo-pseudoisocytidine 7-methylguanosine 2-thio-cytidine N2,2'-O-dimethylguanosine 2-thio-5-methyl-cytidine N2,N2,2'-O-trimethylguanosine 4-thio-pseudoisocytidine 2'-O-ribosylguanosine (phosphate) 4-thio-1-methyl-pseudoisocytidine Wybutosine 4-thio-1-methyl-1-deaza-pseudoisocytidine Peroxywybutosine 1-methyl-1-deaza-pseudoisocytidine Hydroxywybutosine zebularine undermodified hydroxywybutosine 5-aza-zebularine methylwyosine 5-methyl-zebularine queuosine 5-aza-2-thio-zebularine epoxyqueuosine 2-thio-zebularine galactosyl-queuosine 2-methoxy-cytidine mannosyl-queuosine 2-methoxy-5-methyl-cytidine 7-cyano-7-deazaguanosine 4-methoxy-pseudoisocytidine 7-aminomethyl-7-deazaguanosine 4-methoxy-1-methyl-pseudoisocytidine archaeosine 2-aminopurine 5,2'-O-dimethyluridine 2,6-diaminopurine 4-thiouridine 7-deaza-adenine 5-methyl-2-thiouridine 7-deaza-8-aza-adenine 2-thio-2'-O-methyluridine 7-deaza-2-aminopurine 3-(3-amino-3-carboxypropyl)uridine 7-deaza-8-aza-2-aminopurine 5-methoxyuridine 7-deaza-2,6- diaminopurine uridine 5-oxyacetic acid 7-deaza-8-aza-2,6-diarninopurine uridine 5-oxyacetic acid methyl ester 1-methyladenosine 5-(carboxyhydroxymethyl)uridine) N6-isopentenyladenosine 5-(carboxyhydroxymethyl)uridine methyl ester N6-(cis-hydroxyisopentenyl)adenosine 5-methoxycarbonylmethyluridine 2-methylthio-N6-(cis-hydroxyisopentenyl) 5-methoxycarbonylmethyl-2'-O-methyluridine adenosine 5-methoxycarbonylmethyl-2-thiouridine N6-glycinylcarbamoyladenosine 5-aminomethyl-2-thiouridine N6-threonylcarbamoyladenosine 5-methylaminomethyluridine 2-methylthio-N6-threonyl carbamoyladenosine 5-methylaminomethyl-2-thiouridine N6,N6-dimethyladenosine 5-methylaminomethyl-2-selenouridine 7-methyladenine 5-carbamoylmethyluridine 2-methylthio-adenine 5-carbamoylmethyl-2'-O-methyluridine 2-methoxy-adenine 5-carboxymethylaminomethyluridine inosine 5-carboxymethylaminomethyl-2'-O-methyluridine 1-methyl-inosine 5-carboxymethylaminomethyl-2-thiouridine wyosine N4,2'-O-dimethylcytidine wybutosine 5-carboxymethyluridine 7-deaza-guanosine N6,2'-O-dimethyladenosine 7-deaza-8-aza-guanosine N,N6,O-2'-trimethyladenosine 6-thio-guanosine N2,7-dimethylguanosine 6-thio-7-deaza-guanosine N2,N2,7-trimethylguanosine 6-thio-7-deaza-8-aza-guanosine 3,2'-O-dimethyluridine 7-methyl-guanosine 5-methyldihydrouridine 6-thio-7-methyl-guanosine 5-formyl-2'-O-methylcytidine 7-methylinosine 1,2'-O-dimethylguanosine 6-methoxy-guanosine 4-demethylwyosine 1-methylguanosine Isowyosine N2-methylguanosine N6-acetyladenosine N2,N2-dimethylguanosine 8-oxo-guanosine 7-methyl-8-oxo-guanosine 1-methyl-6-thio-guanosine

TABLE 14 Backbone modifications 2'-O-Methyl backbone Peptide Nucleic Acid (PNA) backbone phosphorothioate backbone morpholino backbone carbamate backbone siloxane backbone sulfide backbone sulfoxide backbone sulfone backbone formacetyl backbone thioformacetyl backbone methyleneformacetyl backbone riboacetyl backbone alkene containing backbone sulfamate backbone sulfonate backbone sulfonamide backbone methyleneimino backbone methylenehydrazino backbone amide backbone

TABLE 15 Modified caps m7GpppA m7GpppC m2,7GpppG m2,2,7GpppG m7Gpppm7G m7,2'OmeGpppG m72'dGpppG m7,3'OmeGpppG m7,3'dGpppG GppppG m7GppppG m7GppppA m7GppppC m2,7GppppG m2,2,7GppppG m7Gppppm7G m7,2'OmeGppppG m72'dGppppG m7,3'OmeGppppG m7,3'dGppppG

The nucleotides comprising the template of the gene modifying system can be natural or modified bases, or a combination thereof. For example, the template may contain pseudouridine, dihydrouridine, inosine, 7-methylguanosine, or other modified bases. In some embodiments, the template may contain locked nucleic acid nucleotides. In some embodiments, the modified bases used in the template do not inhibit the reverse transcription of the template. In some embodiments, the modified bases used in the template may improve reverse transcription, e.g., specificity or fidelity.

In some embodiments, an RNA component of the system (e.g., a template RNA or a gRNA) comprises one or more nucleotide modifications. In some embodiments, the modification pattern of a gRNA can significantly affect in vivo activity compared to unmodified or end-modified guides (e.g., as shown in FIG. 1D from Finn et al. Cell Rep 22(9):2227-2235 (2018); incorporated herein by reference in its entirety). Without wishing to be bound by theory, this process may be due, at least in part, to a stabilization of the RNA conferred by the modifications. Non-limiting examples of such modifications may include 2′-O-methyl (2′-O-Me), 2′-O-(2-methoxyethyl) (2′-O-MOE), 2′-fluoro (2′-F), phosphorothioate (PS) bond between nucleotides, G-C substitutions, and inverted abasic linkages between nucleotides and equivalents thereof.

In some embodiments, the template RNA (e.g., at the portion thereof that binds a target site) or the guide RNA comprises a 5′ terminus region. In some embodiments, the template RNA or the guide RNA does not comprise a 5′ terminus region. In some embodiments, the 5′ terminus region comprises a gRNA spacer region, e.g., as described with respect to sgRNA in Briner A E et al, Molecular Cell 56: 333-339 (2014) (incorporated herein by reference in its entirety; applicable herein, e.g., to all guide RNAs). In some embodiments, the 5′ terminus region comprises a 5′ end modification. In some embodiments, a 5′ terminus region with or without a spacer region may be associated with a crRNA, trRNA, sgRNA and/or dgRNA. The gRNA spacer region can, in some instances, comprise a guide region, guide domain, or targeting domain.

In some embodiments, the template RNAs (e.g., at the portion thereof that binds a target site) or guide RNAs described herein comprises any of the sequences shown in Table 4 of WO2018107028A1, incorporated herein by reference in its entirety. In some embodiments, where a sequence shows a guide and/or spacer region, the composition may comprise this region or not. In some embodiments, a guide RNA comprises one or more of the modifications of any of the sequences shown in Table 4 of WO2018107028A1, e.g., as identified therein by a SEQ ID NO. In embodiments, the nucleotides may be the same or different, and/or the modification pattern shown may be the same or similar to a modification pattern of a guide sequence as shown in Table 4 of WO2018107028A1. In some embodiments, a modification pattern includes the relative position and identity of modifications of the gRNA or a region of the gRNA (e.g. 5′ terminus region, lower stem region, bulge region, upper stem region, nexus region, hairpin 1 region, hairpin 2 region, 3′ terminus region). In some embodiments, the modification pattern contains at least 50%, 55%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% of the modifications of any one of the sequences shown in the sequence column of Table 4 of WO2018107028A1, and/or over one or more regions of the sequence. In some embodiments, the modification pattern is at least 50%, 55%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the modification pattern of any one of the sequences shown in the sequence column of Table 4 of WO2018107028A1. In some embodiments, the modification pattern is at least 50%, 55%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% identical over one or more regions of the sequence shown in Table 4 of WO2018107028A1, e.g., in a 5′ terminus region, lower stem region, bulge region, upper stem region, nexus region, hairpin 1 region, hairpin 2 region, and/or 3′ terminus region. In some embodiments, the modification pattern is least 50%, 55%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the modification pattern of a sequence over the 5′ terminus region. In some embodiments, the modification pattern is least 50%, 55%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% identical over the lower stem. In some embodiments, the modification pattern is least 50%, 55%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% identical over the bulge. In some embodiments, the modification pattern is least 50%, 55%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% identical over the upper stem. In some embodiments, the modification pattern is least 50%, 55%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% identical over the nexus. In some embodiments, the modification pattern is least 50%, 55%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% identical over the hairpin 1. In some embodiments, the modification pattern is least 50%, 55%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% identical over the hairpin 2. In some embodiments, the modification pattern is least 50%, 55%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% identical over the 3′ terminus. In some embodiments, the modification pattern differs from the modification pattern of a sequence of Table 4 of WO2018107028A1, or a region (e.g. 5′ terminus, lower stem, bulge, upper stem, nexus, hairpin 1, hairpin 2, 3′ terminus) of such a sequence, e.g., at 0, 1, 2, 3, 4, 5, 6, or more nucleotides. In some embodiments, the gRNA comprises modifications that differ from the modifications of a sequence of Table 4 of WO2018107028A1, e.g., at 0, 1, 2, 3, 4, 5, 6, or more nucleotides. In some embodiments, the gRNA comprises modifications that differ from modifications of a region (e.g. 5′ terminus, lower stem, bulge, upper stem, nexus, hairpin 1, hairpin 2, 3′ terminus) of a sequence of Table 4 of WO2018107028A1, e.g., at 0, 1, 2, 3, 4, 5, 6, or more nucleotides.

In some embodiments, the template RNAs (e.g., at the portion thereof that binds a target site) or the gRNA comprises a 2′-O-methyl (2′-O-Me) modified nucleotide. In some embodiments, the gRNA comprises a 2′-O-(2-methoxy ethyl) (2′-O-moe) modified nucleotide. In some embodiments, the gRNA comprises a 2′-fluoro (2′-F) modified nucleotide. In some embodiments, the gRNA comprises a phosphorothioate (PS) bond between nucleotides. In some embodiments, the gRNA comprises a 5′ end modification, a 3′ end modification, or 5′ and 3′ end modifications. In some embodiments, the 5′ end modification comprises a phosphorothioate (PS) bond between nucleotides. In some embodiments, the 5′ end modification comprises a 2′-O-methyl (2′-O-Me), 2′-O-(2-methoxy ethyl) (2′-O-MOE), and/or 2′-fluoro (2′-F) modified nucleotide. In some embodiments, the 5′ end modification comprises at least one phosphorothioate (PS) bond and one or more of a 2′-O-methyl (2′-O-Me), 2′-O-(2-methoxyethyl) (2′-O-MOE), and/or 2′-fluoro (2′-F) modified nucleotide. The end modification may comprise a phosphorothioate (PS), 2′-O-methyl (2′-O-Me), 2′-O-(2-methoxyethyl) (2′-O-MOE), and/or 2′-fluoro (2′-F) modification. Equivalent end modifications are also encompassed by embodiments described herein. In some embodiments, the template RNA or gRNA comprises an end modification in combination with a modification of one or more regions of the template RNA or gRNA. Additional exemplary modifications and methods for protecting RNA, e.g., gRNA, and formulae thereof, are described in WO2018126176A1, which is incorporated herein by reference in its entirety.

In some embodiments, structure-guided and systematic approaches are used to introduce modifications (e.g., 2′-OMe-RNA, 2′-F-RNA, and PS modifications) to a template RNA or guide RNA, for example, as described in Mir et al. Nat Commun 9:2641 (2018) (incorporated by reference herein in its entirety). In some embodiments, the incorporation of 2′-F-RNAs increases thermal and nuclease stability of RNA:RNA or RNA:DNA duplexes, e.g., while minimally interfering with C3′-endo sugar puckering. In some embodiments, 2′-F may be better tolerated than 2′-OMe at positions where the 2′-OH is important for RNA:DNA duplex stability. In some embodiments, a crRNA comprises one or more modifications that do not reduce Cas9 activity, e.g., C10, C20, or C21 (fully modified), e.g., as described in Supplementary Table 1 of Mir et al. Nat Commun 9:2641 (2018), incorporated herein by reference in its entirety. In some embodiments, a tracrRNA comprises one or more modifications that do not reduce Cas9 activity, e.g., T2, T6, T7, or T8 (fully modified) of Supplementary Table 1 of Mir et al. Nat Commun 9:2641 (2018). In some embodiments, a crRNA comprises one or more modifications (e.g., as described herein) may be paired with a tracrRNA comprising one or more modifications, e.g., C20 and T2. In some embodiments, a gRNA comprises a chimera, e.g., of a crRNA and a tracrRNA (e.g., Jinek et al. Science 337(6096):816-821 (2012)). In embodiments, modifications from the crRNA and tracrRNA are mapped onto the single-guide chimera, e.g., to produce a modified gRNA with enhanced stability.

In some embodiments, gRNA molecules may be modified by the addition or subtraction of the naturally occurring structural components, e.g., hairpins. In some embodiments, a gRNA may comprise a gRNA with one or more 3′ hairpin elements deleted, e.g., as described in WO2018106727, incorporated herein by reference in its entirety. In some embodiments, a gRNA may contain an added hairpin structure, e.g., an added hairpin structure in the spacer region, which was shown to increase specificity of a CRISPR-Cas system in the teachings of Kocak et al. Nat Biotechnol 37(6):657-666 (2019). Additional modifications, including examples of shortened gRNA and specific modifications improving in vivo activity, can be found in US20190316121, incorporated herein by reference in its entirety.

In some embodiments, structure-guided and systematic approaches (e.g., as described in Mir et al. Nat Commun 9:2641 (2018); incorporated herein by reference in its entirety) are employed to find modifications for the template RNA. In embodiments, the modifications are identified with the inclusion or exclusion of a guide region of the template RNA. In some embodiments, a structure of polypeptide bound to template RNA is used to determine non-protein-contacted nucleotides of the RNA that may then be selected for modifications, e.g., with lower risk of disrupting the association of the RNA with the polypeptide. Secondary structures in a template RNA can also be predicted in silico by software tools, e.g., the RNAstructure tool available at rna.urmc.rochester.edu/RNAstructureWeb (Bellaousov et al. Nucleic Acids Res 41:W471-W474 (2013); incorporated by reference herein in its entirety), e.g., to determine secondary structures for selecting modifications, e.g., hairpins, stems, and/or bulges.

Production of Compositions and Systems

As will be appreciated by one of skill, methods of designing and constructing nucleic acid constructs and proteins or polypeptides (such as the systems, constructs and polypeptides described herein) are routine in the art. Generally, recombinant methods may be used. See, in general, Smales & James (Eds.), Therapeutic Proteins: Methods and Protocols (Methods in Molecular Biology), Humana Press (2005); and Crommelin, Sindelar & Meibohm (Eds.), Pharmaceutical Biotechnology: Fundamentals and Applications, Springer (2013). Methods of designing, preparing, evaluating, purifying and manipulating nucleic acid compositions are described in Green and Sambrook (Eds.), Molecular Cloning: A Laboratory Manual (Fourth Edition), Cold Spring Harbor Laboratory Press (2012).

The disclosure provides, in part, a nucleic acid, e.g., vector, encoding a gene modifying polypeptide described herein, a template nucleic acid described herein, or both. In some embodiments, a vector comprises a selective marker, e.g., an antibiotic resistance marker. In some embodiments, the antibiotic resistance marker is a kanamycin resistance marker. In some embodiments, the antibiotic resistance marker does not confer resistance to beta-lactam antibiotics. In some embodiments, the vector does not comprise an ampicillin resistance marker. In some embodiments, the vector comprises a kanamycin resistance marker and does not comprise an ampicillin resistance marker. In some embodiments, a vector encoding a gene modifying polypeptide is integrated into a target cell genome (e.g., upon administration to a target cell, tissue, organ, or subject). In some embodiments, a vector encoding a gene modifying polypeptide is not integrated into a target cell genome (e.g., upon administration to a target cell, tissue, organ, or subject). In some embodiments, a vector encoding a template nucleic acid (e.g., template RNA) is not integrated into a target cell genome (e.g., upon administration to a target cell, tissue, organ, or subject). In some embodiments, if a vector is integrated into a target site in a target cell genome, the selective marker is not integrated into the genome. In some embodiments, if a vector is integrated into a target site in a target cell genome, genes or sequences involved in vector maintenance (e.g., plasmid maintenance genes) are not integrated into the genome. In some embodiments, if a vector is integrated into a target site in a target cell genome, transfer regulating sequences (e.g., inverted terminal repeats, e.g., from an AAV) are not integrated into the genome. In some embodiments, administration of a vector (e.g., encoding a gene modifying polypeptide described herein, a template nucleic acid described herein, or both) to a target cell, tissue, organ, or subject results in integration of a portion of the vector into one or more target sites in the genome(s) of said target cell, tissue, organ, or subject. In some embodiments, less than 99, 95, 90, 80, 70, 60, 50, 40, 30, 20, 10, 5, 4, 3, 2, or 1% of target sites (e.g., no target sites) comprising integrated material comprise a selective marker (e.g., an antibiotic resistance gene), a transfer regulating sequence (e.g., an inverted terminal repeat, e.g., from an AAV), or both from the vector.

Exemplary methods for producing a therapeutic pharmaceutical protein or polypeptide described herein involve expression in mammalian cells, although recombinant proteins can also be produced using insect cells, yeast, bacteria, or other cells under control of appropriate promoters. Mammalian expression vectors may comprise non-transcribed elements such as an origin of replication, a suitable promoter, and other 5′ or 3′ flanking non-transcribed sequences, and 5′ or 3′ non-translated sequences such as necessary ribosome binding sites, a polyadenylation site, splice donor and acceptor sites, and termination sequences. DNA sequences derived from the SV40 viral genome, for example, SV40 origin, early promoter, splice, and polyadenylation sites may be used to provide other genetic elements required for expression of a heterologous DNA sequence. Appropriate cloning and expression vectors for use with bacterial, fungal, yeast, and mammalian cellular hosts are described in Green & Sambrook, Molecular Cloning: A Laboratory Manual (Fourth Edition), Cold Spring Harbor Laboratory Press (2012).

Various mammalian cell culture systems can be employed to express and manufacture recombinant protein. Examples of mammalian expression systems include CHO, COS, HEK293, HeLA, and BHK cell lines. Processes of host cell culture for production of protein therapeutics are described in Zhou and Kantardjieff (Eds.), Mammalian Cell Cultures for Biologics Manufacturing (Advances in Biochemical Engineering Biotechnology), Springer (2014). Compositions described herein may include a vector, such as a viral vector, e.g., a lentiviral vector, encoding a recombinant protein. In some embodiments, a vector, e.g., a viral vector, may comprise a nucleic acid encoding a recombinant protein.

Purification of protein therapeutics is described in Franks, Protein Biotechnology: Isolation, Characterization, and Stabilization, Humana Press (2013); and in Cutler, Protein Purification Protocols (Methods in Molecular Biology), Humana Press (2010).

The disclosure also provides compositions and methods for the production of template nucleic acid molecules (e.g., template RNAs) with specificity for a gene modifying polypeptide and/or a genomic target site. In an aspect, the method comprises production of RNA segments including an upstream homology segment, a heterologous object sequence segment, a gene modifying polypeptide binding motif, and a gRNA segment.

Therapeutic Applications

In some embodiments, a gene modifying system as described herein can be used to modify a cell (e.g., an animal cell, plant cell, or fungal cell). In some embodiments, a gene modifying system as described herein can be used to modify a mammalian cell (e.g., a human cell). In some embodiments, a gene modifying system as described herein can be used to modify a cell from a livestock animal (e.g., a cow, horse, sheep, goat, pig, llama, alpaca, camel, yak, chicken, duck, goose, or ostrich). In some embodiments, a gene modifying system as described herein can be used as a laboratory tool or a research tool, or used in a laboratory method or research method, e.g., to modify an animal cell, e.g., a mammalian cell (e.g., a human cell), a plant cell, or a fungal cell.

By integrating coding genes into a RNA sequence template, the gene modifying system can address therapeutic needs, for example, by providing expression of a therapeutic transgene in individuals with loss-of-function mutations, by replacing gain-of-function mutations with normal transgenes, by providing regulatory sequences to eliminate gain-of-function mutation expression, and/or by controlling the expression of operably linked genes, transgenes and systems thereof. In certain embodiments, the RNA sequence template encodes a promotor region specific to the therapeutic needs of the host cell, for example a tissue specific promotor or enhancer. In still other embodiments, a promotor can be operably linked to a coding sequence.

In some embodiments, an insertion, deletion, substitution, or combination thereof, increases or decreases expression (e.g. transcription or translation) of a target gene. In some embodiments, an insertion, deletion, substitution, or combination thereof, increases or decreases expression (e.g. transcription or translation) of a target gene by altering, adding, or deleting sequences in a promoter or enhancer, e.g. sequences that bind transcription factors. In some embodiments, an insertion, deletion, substitution, or combination thereof alters translation of a target gene (e.g. alters an amino acid sequence), inserts or deletes a start or stop codon, alters or fixes the translation frame of a gene. In some embodiments, an insertion, deletion, substitution, or combination thereof alters splicing of a target gene, e.g. by inserting, deleting, or altering a splice acceptor or donor site. In some embodiments, an insertion, deletion, substitution, or combination thereof alters transcript or protein half-life. In some embodiments, an insertion, deletion, substitution, or combination thereof, alters, increases, decreases the activity of a target gene, e.g. a protein encoded by the target gene.

Compensatory Edits

In some embodiments, the systems or methods provided herein can be used to introduce a compensatory edit. In some embodiments, the compensatory edit is at a position of a gene associated with a disease or disorder, which is different from the position of a disease-causing mutation. In some embodiments, the compensatory mutation is not in the gene containing the causative mutation. In some embodiments, the compensatory edit can negate or compensate for a disease-causing mutation. In some embodiments, the compensatory edit can be introduced by the system or methods provided herein to suppress or reverse the mutant effect of a disease-causing mutation.

Regulatory Edits

In some embodiments, the systems or methods provided herein can be used to introduce a regulatory edit. In some embodiments, the regulatory edit is introduced to a regulatory sequence of a gene, for example, a gene promoter, gene enhancer, gene repressor, or a sequence that regulates gene splicing. In some embodiments, the regulatory edit increases or decreases the expression level of a target gene. In some embodiments, the target gene is the same as the gene containing a disease-causing mutation. In some embodiments, the target gene is different from the gene containing a disease-causing mutation.

Repeat Expansion Diseases

In some embodiments, the systems or methods provided herein can be used to treat a repeat expansion disease. In some embodiments, the systems or methods provided herein, for example, those comprising gene modifying polypeptides, can be used to treat repeat expansion diseases by resetting the number of repeats at the locus according to a customized RNA template.

Administration and Delivery

The compositions and systems described herein may be used in vitro or in vivo. In some embodiments the system or components of the system are delivered to cells (e.g., mammalian cells, e.g., human cells), e.g., in vitro or in vivo. In some embodiments, the cells are eukaryotic cells, e.g., cells of a multicellular organism, e.g., an animal, e.g., a mammal (e.g., human, swine, bovine), a bird (e.g., poultry, such as chicken, turkey, or duck), or a fish. In some embodiments, the cells are non-human animal cells (e.g., a laboratory animal, a livestock animal, or a companion animal). In some embodiments, the cell is a stem cell (e.g., a hematopoietic stem cell), a fibroblast, or a T cell. In some embodiments, the cell is an immune cell, e.g., a T cell (e.g., a Treg, CD4, CD8, γδ, or memory T cell), B cell (e.g., memory B cell or plasma cell), or NK cell. In some embodiments, the cell is a non-dividing cell, e.g., a non-dividing fibroblast or non-dividing T cell. In some embodiments, the cell is an HSC and p53 is not upregulated or is upregulated by less than 10%, 5%, 2%, or 1%, e.g., as determined according to the method described in Example 30 of PCT/US2019/048607. The skilled artisan will understand that the components of the gene modifying system may be delivered in the form of polypeptide, nucleic acid (e.g., DNA, RNA), and combinations thereof.

In one embodiment the system and/or components of the system are delivered as nucleic acid. For example, the gene modifying polypeptide may be delivered in the form of a DNA or RNA encoding the polypeptide, and the template RNA may be delivered in the form of RNA or its complementary DNA to be transcribed into RNA. In some embodiments the system or components of the system are delivered on 1, 2, 3, 4, or more distinct nucleic acid molecules. In some embodiments the system or components of the system are delivered as a combination of DNA and RNA. In some embodiments the system or components of the system are delivered as a combination of DNA and protein. In some embodiments the system or components of the system are delivered as a combination of RNA and protein. In some embodiments the gene modifying polypeptide is delivered as a protein.

In some embodiments the system or components of the system are delivered to cells, e.g. mammalian cells or human cells, using a vector. The vector may be, e.g., a plasmid or a virus. In some embodiments, delivery is in vivo, in vitro, ex vivo, or in situ. In some embodiments the virus is an adeno associated virus (AAV), a lentivirus, or an adenovirus. In some embodiments the system or components of the system are delivered to cells with a viral-like particle or a virosome. In some embodiments the delivery uses more than one virus, viral-like particle or virosome.

In one embodiment, the compositions and systems described herein can be formulated in liposomes or other similar vesicles. Liposomes are spherical vesicle structures composed of a uni- or multilamellar lipid bilayer surrounding internal aqueous compartments and a relatively impermeable outer lipophilic phospholipid bilayer. Liposomes may be anionic, neutral or cationic. Liposomes are biocompatible, nontoxic, can deliver both hydrophilic and lipophilic drug molecules, protect their cargo from degradation by plasma enzymes, and transport their load across biological membranes and the blood brain barrier (BBB) (see, e.g., Spuch and Navarro, Journal of Drug Delivery, vol. 2011, Article ID 469679, 12 pages, 2011. doi:10.1155/2011/469679 for review).

Vesicles can be made from several different types of lipids; however, phospholipids are most commonly used to generate liposomes as drug carriers. Methods for preparation of multilamellar vesicle lipids are known in the art (see for example U.S. Pat. No. 6,693,086, the teachings of which relating to multilamellar vesicle lipid preparation are incorporated herein by reference). Although vesicle formation can be spontaneous when a lipid film is mixed with an aqueous solution, it can also be expedited by applying force in the form of shaking by using a homogenizer, sonicator, or an extrusion apparatus (see, e.g., Spuch and Navarro, Journal of Drug Delivery, vol. 2011, Article ID 469679, 12 pages, 2011. doi:10.1155/2011/469679 for review). Extruded lipids can be prepared by extruding through filters of decreasing size, as described in Templeton et al., Nature Biotech, 15:647-652, 1997, the teachings of which relating to extruded lipid preparation are incorporated herein by reference.

A variety of nanoparticles can be used for delivery, such as a liposome, a lipid nanoparticle, a cationic lipid nanoparticle, an ionizable lipid nanoparticle, a polymeric nanoparticle, a gold nanoparticle, a dendrimer, a cyclodextrin nanoparticle, a micelle, or a combination of the foregoing.

Lipid nanoparticles are an example of a carrier that provides a biocompatible and biodegradable delivery system for the pharmaceutical compositions described herein. Nanostructured lipid carriers (NLCs) are modified solid lipid nanoparticles (SLNs) that retain the characteristics of the SLN, improve drug stability and loading capacity, and prevent drug leakage. Polymer nanoparticles (PNPs) are an important component of drug delivery. These nanoparticles can effectively direct drug delivery to specific targets and improve drug stability and controlled drug release. Lipid-polymer nanoparticles (PLNs), a type of carrier that combines liposomes and polymers, may also be employed. These nanoparticles possess the complementary advantages of PNPs and liposomes. A PLN is composed of a core-shell structure; the polymer core provides a stable structure, and the phospholipid shell offers good biocompatibility. As such, the two components increase the drug encapsulation efficiency rate, facilitate surface modification, and prevent leakage of water-soluble drugs. For a review, see, e.g., Li et al. 2017, Nanomaterials 7, 122; doi:10.3390/nano7060122.

Exosomes can also be used as drug delivery vehicles for the compositions and systems described herein. For a review, see Ha et al. July 2016. Acta Pharmaceutica Sinica B. Volume 6, Issue 4, Pages 287-296; doi.org/10.1016/j.apsb.2016.02.001.

Fusosomes interact and fuse with target cells, and thus can be used as delivery vehicles for a variety of molecules. They generally consist of a bilayer of amphipathic lipids enclosing a lumen or cavity and a fusogen that interacts with the amphipathic lipid bilayer. The fusogen component has been shown to be engineerable in order to confer target cell specificity for the fusion and payload delivery, allowing the creation of delivery vehicles with programmable cell specificity (see for example Patent Application WO2020014209, the teachings of which relating to fusosome design, preparation, and usage are incorporated herein by reference).

In some embodiments, the protein component(s) of the gene modifying system may be pre-associated with the template nucleic acid (e.g., template RNA). For example, in some embodiments, the gene modifying polypeptide may be first combined with the template nucleic acid (e.g., template RNA) to form a ribonucleoprotein (RNP) complex. In some embodiments, the RNP may be delivered to cells via, e.g., transfection, nucleofection, virus, vesicle, LNP, exosome, fusosome.

A gene modifying system can be introduced into cells, tissues and multicellular organisms. In some embodiments the system or components of the system are delivered to the cells via mechanical means or physical means.

Formulation of protein therapeutics is described in Meyer (Ed.), Therapeutic Protein Drug Products: Practical Approaches to formulation in the Laboratory, Manufacturing, and the Clinic, Woodhead Publishing Series (2012).

Tissue Specific Activity/Administration

In some embodiments, a system described herein can make use of one or more feature (e.g., a promoter or microRNA binding site) to limit activity in off-target cells or tissues.

In some embodiments, a nucleic acid described herein (e.g., a template RNA or a DNA encoding a template RNA) comprises a promoter sequence, e.g., a tissue specific promoter sequence. In some embodiments, the tissue-specific promoter is used to increase the target-cell specificity of a gene modifying system. For instance, the promoter can be chosen on the basis that it is active in a target cell type but not active in (or active at a lower level in) a non-target cell type. Thus, even if the promoter integrated into the genome of a non-target cell, it would not drive expression (or only drive low level expression) of an integrated gene. A system having a tissue-specific promoter sequence in the template RNA may also be used in combination with a microRNA binding site, e.g., in the template RNA or a nucleic acid encoding a gene modifying protein, e.g., as described herein. A system having a tissue-specific promoter sequence in the template RNA may also be used in combination with a DNA encoding a gene modifying polypeptide, driven by a tissue-specific promoter, e.g., to achieve higher levels of gene modifying protein in target cells than in non-target cells. In some embodiments, e.g., for liver indications, a tissue-specific promoter is selected from Table 3 of WO2020014209, incorporated herein by reference.

In some embodiments, a nucleic acid described herein (e.g., a template RNA or a DNA encoding a template RNA) comprises a microRNA binding site. In some embodiments, the microRNA binding site is used to increase the target-cell specificity of a gene modifying system. For instance, the microRNA binding site can be chosen on the basis that is recognized by a miRNA that is present in a non-target cell type, but that is not present (or is present at a reduced level relative to the non-target cell) in a target cell type. Thus, when the template RNA is present in a non-target cell, it would be bound by the miRNA, and when the template RNA is present in a target cell, it would not be bound by the miRNA (or bound but at reduced levels relative to the non-target cell). While not wishing to be bound by theory, binding of the miRNA to the template RNA may interfere with its activity, e.g., may interfere with insertion of the heterologous object sequence into the genome. Accordingly, the system would edit the genome of target cells more efficiently than it edits the genome of non-target cells, e.g., the heterologous object sequence would be inserted into the genome of target cells more efficiently than into the genome of non-target cells, or an insertion or deletion is produced more efficiently in target cells than in non-target cells. A system having a microRNA binding site in the template RNA (or DNA encoding it) may also be used in combination with a nucleic acid encoding a gene modifying polypeptide, wherein expression of the gene modifying polypeptide is regulated by a second microRNA binding site, e.g., as described herein. In some embodiments, e.g., for liver indications, a miRNA is selected from Table 4 of WO2020014209, incorporated herein by reference.

In some embodiments, the template RNA comprises a microRNA sequence, an siRNA sequence, a guide RNA sequence, or a piwi RNA sequence.

Promoters

In some embodiments, one or more promoter or enhancer elements are operably linked to a nucleic acid encoding a gene modifying protein or a template nucleic acid, e.g., that controls expression of the heterologous object sequence. In certain embodiments, the one or more promoter or enhancer elements comprise cell-type or tissue specific elements. In some embodiments, the promoter or enhancer is the same or derived from the promoter or enhancer that naturally controls expression of the heterologous object sequence. For example, the ornithine transcarbamylase promoter and enhancer may be used to control expression of the ornithine transcarbamylase gene in a system or method provided by the invention for correcting ornithine transcarbamylase deficiencies. In some embodiments, the promoter is a promoter of Table 16 or 17 or a functional fragment or variant thereof.

Exemplary tissue specific promoters that are commercially available can be found, for example, at a uniform resource locator (e.g., www.invivogen.com/tissue-specific-promoters). In some embodiments, a promoter is a native promoter or a minimal promoter, e.g., which consists of a single fragment from the 5′ region of a given gene. In some embodiments, a native promoter comprises a core promoter and its natural 5′ UTR. In some embodiments, the 5′ UTR comprises an intron. In other embodiments, these include composite promoters, which combine promoter elements of different origins or were generated by assembling a distal enhancer with a minimal promoter of the same origin.

Exemplary cell or tissue specific promoters are provided in the tables, below, and exemplary nucleic acid sequences encoding them are known in the art and can be readily accessed using a variety of resources, such as the NCBI database, including RefSeq, as well as the Eukaryotic Promoter Database (//epd.epfl.ch//index.php).

TABLE 16 Exemplary cell or tissue-specific promoters Promoter Target cells B29 Promoter B cells CD14 Promoter Monocytic Cells CD43 Promoter Leukocytes and platelets CD45 Promoter Hematopoeitic cells CD68 promoter macrophages Desmin promoter muscle cells Elastase-1 promoter pancreatic acinar cells Endoglin promoter endothelial cells fibronectin promoter differentiating cells, healing tissue Flt-1 promoter endothelial cells GFAP promoter Astrocytes GPIIB promoter megakaryocytes ICAM-2 Promoter Endothelial cells INF-Beta promoter Hematopoeitic cells Mb promoter muscle cells Nphs1 promoter podocytes OG-2 promoter Osteoblasts, Odonblasts SP-B promoter Lung Syn 1 promoter Neurons WASP promoter Hematopoeitic cells SV40/bAlb promoter Liver SV40/bAlb promoter Liver SV40/Cd3 promoter Leukocytes and platelets SV40/CD45 promoter hematopoeitic cells NSE/RU5' promoter Mature Neurons

TABLE 17 Additional exemplary cell or tissue-specific promoters Promoter Gene Description Gene Specificity APOA2 Apolipoprotein A-II Hepatocytes (from hepatocyte progenitors) SERPINA1 Serpin peptidase inhibitor, clade A (alpha-1 Hepatocytes (hAAT) antiproteinase, antitrypsin), member 1 (from definitive endoderm (also named alpha 1 anti-tryps in) stage) CYP3A Cytochrome P450, family 3, subfamily A, polypeptide Mature Hepatocytes MIR122 MicroRNA 122 Hepatocytes (from early stage embryonic liver cells) and endoderm Pancreatic specific promoters INS Insulin Pancreatic beta cells (from definitive endoderm stage) IRS2 Insulin receptor substrate 2 Pancreatic beta cells Pdx1 Pancreatic and duodenal Pancreas homeobox 1 (from definitive endoderm stage) Alx3 Aristaless-like homeobox 3 Pancreatic beta cells (from definitive endoderm stage) Ppy Pancreatic polypeptide PP pancreatic cells (gamma cells) Cardiac specific promoters Myh6 (aMHC) Myosin, heavy chain 6, cardiac muscle, alpha Late differentiation marker of cardiac muscle cells (atrial specificity) MYL2 (MLC-2v) Myosin, light chain 2, regulatory, cardiac, slow Late differentiation marker of cardiac muscle cells (ventricular specificity) ITNNI3 Troponin I type 3 (cardiac) Cardiomyocytes (cTnl) (from immature state) ITNNI3 Troponin I type 3 (cardiac) Cardiomyocytes (cTnl) (from immature state) NPPA (ANF) Natriuretic peptide precursor A (also named Atrial Natriuretic Atrial specificity in adult cells Factor) Slc8a1 (Ncx1) Solute carrier family B (sodium/calcium exchanger), member 1 Cardiomyocytes from early developmental stages CNS specific promoters SYN1 (hSyn) Synapsin I Neurons GFAP Glial fibrillary acidic protein Astrocytes INA Internexin neuronal intermediate filament protein, alpha (a- Neuroprogenitors internexin) NES Nestin Neuroprogenitors and ectoderm MOBP Myelin-associated oligodendrocyte basic protein Oligodendrocytes MBP Myelin basic protein Oligodendrocytes TH Tyrosine hydroxylase Dopaminergic neurons FOXA2 (HNF3 Forkhead box A2 Dopaminergic neurons (also used as a marker of endoderm) beta) Skin specific promoters FLG Filaggrin Keratinocytes from granular layer K14 Keratin 14 Keratinocytes from granular and basal layers TGM3 Transglutaminase 3 Keratinocytes from granular layer Immune cell specific promoters ITGAM Integrin, alpha M (complement Monocytes, macrophages , granulocytes , (CD11B) component 3 receptor 3 subunit) natural killer cells Urogential cell specific promoters Pbsn Probasin Prostatic epithelium Upk2 Uroplakin 2 Bladder Sbp Spermine binding protein Prostate Fer1|4 Fer-1-like 4 Bladder Endothelial cell specific promoters ENG Endoglin Endothelial cells Pluripotent and embryonic cell specific promoters Promoter Gene Description Gene Specificity Oct. 4 (POU5F1) POU class 5 homeobox 1 Pluripotent cells (germ cells, ES cells, iPS cells) NANOG Nanog homeobox Pluripotent cells (ES cells, iPS cells) Synthetic Oct. 4 Synthetic promoter based on a Oct-4 core enhancer element Pluripotent cells (ES cells, iPS cells) T brachyury Brachyury Mesoderm NES Nestin Neuroprogenitors and Ectoderm SOX17 SRY (sex determining region Y)-box 17 Endoderm FOXA2 (HNFJ Forkhead box A2 Endoderm (also used as a marker of dopaminergic neurons) beta) MIR122 MicroRNA 122 Endoderm and hepatocytes (from early stage embryonic liver cells~

Depending on the host/vector system utilized, any of a number of suitable transcription and translation control elements, including constitutive and inducible promoters, transcription enhancer elements, transcription terminators, etc. may be used in the expression vector (see e.g. Bitter et al. (1987) Methods in Enzymology, 153:516-544: incorporated herein by reference in its entirety).

In some embodiments, a nucleic acid encoding a gene modifying protein or template nucleic acid is operably linked to a control element, e.g, a transcriptional control element, such as a promoter. The transcriptional control element may, in some embodiment, be functional in either a eukaryotic cell, e.g., a mammalian ceil; or a prokaryotic cell (e.g., bacterial or archaeal cell). In some embodiments, a nucleotide sequence encoding a polypeptide is operably linked to multiple control elements, e.g., that allow expression of the nucleotide sequence encoding the polypeptide in both prokaryotic and eukaryotic cells.

For illustration purposes, examples of spatially restricted promoters include, but are not limited to, neuron-specific promoters, adipocyte-specific promoters, cardiomyocyte-specific promoters, smooth muscle-specific promoters, photoreceptor-specific promoters, etc. Neuron-specific spatially restricted promoters include, but are not limited to, a neuron-specific enolase (NSE) promoter (see. e.g., EMBL HSENO2, X51956); an aromatic amino acid decarboxylase (AADC) promoter, a neurofilament promoter (see, e.g., GenBank HUMNFL, L04147); a synapsin promoter (see, e.g., GenBank HUMSYNIB. M55301); a thy-1 promoter (see, e.g., Chen et al (1987) Cell 51:7-19; and Llewellyn, et al (2010) Nat. Med. 16(10):1161-1166): a serotonin receptor promoter (see, e.g., GenBank S62283); a tyrosine hydroxylase promoter (TH) (see, e.g., Oh et al. (2009) Gene Ther 16:437; Sasaoka et al. (1992) Mol. Brain Res. 16:274; Boundy et al. (1998) J. Neurosci. 18:9989; and Kaneda et al. (1991) Neuron 6:583-594); a GnRH promoter (see, e.g., Radovick et al. (1991) Proc. Natl. Acad. Sci. USA 88:3402-3406); an L7 promoter (see, e.g., Oberdick et al. (1990) Science 248:223-226); a DNMT promoter (see, e.g., Bartge et al. (1988) Proc. Natl. Acad. Sci. USA 85:3648-3652); an enkephalin promoter (see, e.g., Comb et al. (1988) EMBO J. 17:3793-3805); a myelin basic protein (MBP) promoter; a Ca2+-calmodulin-dependent protein kinase II-alpha (CamKIIα) promoter (see, e.g., Mayford et al. (1996) Proc. Natl. Acad. Sci. USA 93:13250; and Casanova et al. (2001) Genesis 31:37); a CMV enhancer/platelet-derived growth factor-β promoter (see, e.g., Liu et al. (2004) Gene Therapy 11:52-60); and the like.

Adipocyte-specific spatially restricted promoters include, but are not limited to, the aP2 gene promoter/enhancer, e.g., a region from −5.4 kb to +21 bp of a human aP2 gene (see, e.g., Tozzo et al. (1997) Endocrinol. 138:16042 Ross et al. (1990) Proc. Natl. Acad. Sci. USA 87:9590; and Pavjani et al. (2005) Nat. Med. 11:797); a glucose transporter-4 (GLUT4) promoter (see, e.g., Knight et al. (2003) Proc. Natl. Acad. Sci. USA 100:14725); a fatty acid translocase (FAT/CD36) promoter (see, e.g., Kuriki et al. (2002) Biol Pharm. Bull. 25:1476; and Sato et al (2002) J. Biol. Chem. 277:15703); a stearoyl-CoA desaturase-1 (SCD1) promoter (Tabor et al. (1999) J. Biol. Chem. 274:20603); a leptin promoter (see, e.g., Mason et al. (1998) Endocrinol. 139:1013; and Chen et al. (1999) Biochem. Biophys. Res. Comm. 262:187); an adiponectin promoter (see, e.g., Kita et al. (2005) Biochem. Biophys. Res. Comm. 331:484; and Chakrabarti (2010) Endocrinol. 151:2408); an adipsin promoter (see, e.g., Platt et al. (1989) Proc. Natl. Acad. Sci. USA 86:7490); a resistin promoter (see, e.g., Seo et al. (2003) Molec. Endocrinal. 17:1522); and the like.

Cardiomyocyte-specific spatially restricted promoters include, but are not limited to, control sequences derived from the following genes: myosin light chain-2, α-myosin heavy chain, AE3, cardiac troponin C, cardiac actin, and the like. Franz et al. (1997) Cardiovasc. Res. 35:560-566: Robbins t al, (1995) Ann. N.Y. Acad. Sci. 752:492-505; Linn et al. (1995) Circ. Res. 76:584-591; Parmacek et al. (1994) Mol. Cell. Biol. 14:1870-1885; Hunter et al. (1993) Hypertension 22:608-617; and Sartorelli et al. (1992) Proc. Natl. Acad. Sci. USA 89:4047-4051.

Smooth muscle-specific spatially restricted promoters include, but are not limited to, an SM22α promoter (see, e.g., Akyürek et al. (2000) Mol. Med. 6:983; and U.S. Pat. No. 7,169,874); a smoothelin promoter (see. e.g., WO 2001/018048); an α-smooth muscle actin promoter; and the like. For example, a 0.4 kb region of the SM22α promoter, within which lie two CArG elements, has been shown to mediate vascular smooth muscle cell-specific expression (see, e.g., Kim, et al. (1997) Mol. Cell Biol. 17, 2266-2278; Li, et al., (1996) J. Cell Biol. 132, 849-859; and Moessler, et al. (1996) Development 122, 2415-2425).

Photoreceptor-specific spatially restricted promoters include, but are not limited to, a rhodopsin promoter; a rhodopsin kinase promoter (Young et al. (2003) Ophthalmol. Vis. Sci. 44:4076); a beta phosphodiesterase gene promoter (Nicoud et al. (2007) J. Gene Med. 9:1015); a retinitis pigmentosa gene promoter (Nicoud et al. (2007)supra); an interphotoreceptor retinoid-binding protein (IRBP) gene enhancer (Nicoud et al. (2007)supra); an IRBP gene promoter (Yokoyama et al. (1992) Exp Eye Res. 55:225); and the like.

In some embodiments, a gene modifying system, e.g., DNA encoding a gene modifying polypeptide, DNA encoding a template RNA, or DNA or RNA encoding a heterologous object sequence, is designed such that one or more elements is operably linked to a tissue-specific promoter, e.g., a promoter that is active in T-cells. In further embodiments, the T-cell active promoter is inactive in other cell types, e.g., B-cells, NK cells. In some embodiments, the T-cell active promoter is derived from a promoter for a gene encoding a component of the T-cell receptor, e.g., TRAC, TRBC, TRGC, TRDC. In some embodiments, the T-cell active promoter is derived from a promoter for a gene encoding a component of a T-cell-specific cluster of differentiation protein, e.g., CD3, e.g., CD3D, CD3E, CD3G, CD3Z. In some embodiments, T-cell-specific promoters in gene modifying systems are discovered by comparing publicly available gene expression data across cell types and selecting promoters from the genes with enhanced expression in T-cells. In some embodiments, promoters may be selecting depending on the desired expression breadth, e.g., promoters that are active in T-cells only, promoters that are active in NK cells only, promoters that are active in both T-cells and NK cells.

Cell-specific promoters known in the art may be used to direct expression of a gene modifying protein, e.g., as described herein. Nonlimiting exemplary mammalian cell-specific promoters have been characterized and used in mice expressing Cre recombinase in a cell-specific manner, Certain nonlimiting exemplary mammalian cell-specific promoters are listed in Table 1 of U.S. Pat. No. 9,845,481, incorporated herein by reference.

In some embodiments, a vector as described herein comprises an expression cassette. Typically, an expression cassette comprises the nucleic acid molecule of the instant invention operatively linked to a promoter sequence. For example, a promoter is operatively linked with a coding sequence when it is capable of affecting the expression of that coding sequence (e.g., the coding sequence is under the transcriptional control of the promoter). Encoding sequences can be operatively linked to regulatory sequences in sense or antisense orientation. In certain embodiments, the promoter is a heterologous promoter. In certain embodiments, an expression cassette may comprise additional elements, for example, an intron, an enhancer, a polyadenylation site, a woodchuck response element (WRE), and/or other elements known to affect expression levels of the encoding sequence. A promoter typically controls the expression of a coding sequence or functional RNA. In certain embodiments, a promoter sequence comprises proximal and more distal upstream elements and can further comprise an enhancer element. An enhancer can typically stimulate promoter activity and may be an innate element of the promoter or a heterologous element inserted to enhance the level or tissue-specificity of a promoter. In certain embodiments, the promoter is derived in its entirety from a native gene. In certain embodiments, the promoter is composed of different elements derived from different naturally occurring promoters. In certain embodiments, the promoter comprises a synthetic nucleotide sequence. It will be understood by those skilled in the art that different promoters will direct the expression of a gene in different tissues or cell types, or at different stages of development, or in response to different environmental conditions or to the presence or the absence of a drug or transcriptional co-factor. Ubiquitous, cell-type-specific, tissue-specific, developmental stage-specific, and conditional promoters, for example, drug-responsive promoters (e.g., tetracycline-responsive promoters) are well known to those of skill in the art. Exemplary promoters include, but are not limited to, the phosphoglycerate kinase (PKG) promoter, CAG (composite of the CMV enhancer the chicken beta actin promoter (CBA) and the rabbit beta globin intron), NSE (neuronal specific enolase), synapsin or NeuN promoters, the SV40 early promoter, mouse mammary tumor virus LTR promoter; adenovirus major late promoter (Ad MLP), a herpes simplex virus (HSV) promoter, a cytomegalovirus (CMV) promoter such as the CMV immediate early promoter region (CMVIE), SFFV promoter, rous sarcoma virus (RSV) promoter, synthetic promoters, hybrid promoters, and the like. Other promoters can be of human origin or from other species, including: from mice. Common promoters include, e.g., the human cytomegalovirus (CMV) immediate early gene promoter, the SV40 early promoter, the Rous sarcoma virus long terminal repeat, [beta]-actin, rat insulin promoter, the phosphoglycerate kinase promoter, the human alpha-1 antitrypsin (hAAT) promoter, the transthyretin promoter, the TBG promoter and other liver-specific promoters, the desmin promoter and similar muscle-specific promoters, the EF1-alpha promoter, hybrid promoters with multi-tissue specificity, promoters specific for neurons like synapsin and glyceraldehyde-3-phosphate dehydrogenase promoter, all of which are promoters well known and readily available to those of skill in the art, can be used to obtain high-level expression of the coding sequence of interest. In addition, sequences derived from non-viral genes, such as the murine metallothionein gene, will also find use herein. Such promoter sequences are commercially available from, e.g., Stratagene (San Diego, CA). Additional exemplary promoter sequences are described, for example, in WO2018213786A1 (incorporated by reference herein in its entirety).

In some embodiments, the apolipoprotein E enhancer (ApoE) or a functional fragment thereof is used, e.g., to drive expression in the liver. In some embodiments, two copies of the ApoE enhancer or a functional fragment thereof are used. In some embodiments, the ApoE enhancer or functional fragment thereof is used in combination with a promoter, e.g., the human alpha-1 antitrypsin (hAAT) promoter.

In some embodiments, the regulatory sequences impart tissue-specific gene expression capabilities. In some cases, the tissue-specific regulator-sequences bind tissue-specific transcription factors that induce transcription in a tissue specific manner. Various tissue-specific regulatory sequences (e.g., promoters, enhancers, etc.) are known in the art. Exemplary tissue-specific regulatory sequences include, but are not limited to, the following tissue-specific promoters: a liver-specific thyroxin binding globulin (TBG) promoter, an insulin promoter, a glucagon promoter, a somatostatin promoter, a pancreatic polypeptide (PPY) promoter, a synapsin-1 (Syn) promoter, a creatine kinase (MCK) promoter, a mammalian desmin (DES) promoter, a α-myosin heavy chain (a-MHC) promoter, or a cardiac Troponin T (cTnT) promoter. Other exemplary promoters include Beta-actin promoter, hepatitis B virus core promoter, Sandig et al, Gene Ther., 3:1002-9 (1996); alpha-fetoprotein (AFP) promoter, Arbuthnot et al., Hum. Gene Ther., 7:1503-14 (1996)), bone osteocalcin promoter (Stein et al., Mol. Biol. Rep., 24:185-96 (1997)); bone sialoprotein promoter (Chen et al., J. Bone Miner. Res., 11:654-64 (1996)) CD2 promoter (Hansal et al., J. Immunol., 161:1063-8 (1998); immunoglobulin heavy chain promoter; T cell receptor α-chain promoter, neuronal such as neuron-specific enolase (NSE) promoter (Andersen et al., Cell. Mol Neurobiol., 13:503-15 (1993)), neurofilament light-chain gene promoter (Piccioli et al, Proc. Natl. Acad. Sci. USA, 88:5611-5 (1991)), and the neuron-specific, vgf gene promoter (Piccioli et al., Neuron, 15:373-84 (1995)), and others. Additional exemplary promoter sequences are described, for example, in U.S. patent Ser. No. 10/300,146 (incorporated herein by reference in its entirety). In some embodiments, a tissue-specific regulatory element, e.g., a tissue-specific promoter, is selected from one known to be operably linked to a gene that is highly expressed in a given tissue. e.g., as measured by RNA-seq or protein expression data, or a combination thereof. Methods for analyzing tissue specificity by expression are taught in Fagerberg et al. Mol Cell Proteomes 13 (2:307-406 (2014), which is incorporated herein by reference in its entirety.

In some embodiments, a vector described herein is a multicistronic expression construct, Multicistronic expression constructs include, for example, constructs harboring a first expression cassette, e.g. comprising a first promoter and a first encoding nucleic acid sequence, and a second expression cassette, e.g. comprising a second promoter and a second encoding nucleic acid sequence. Such multicistronic expression constructs may, in some instances, be particularly useful in the delivery of non-translated gene products, such as hairpin RNAs, together with a polypeptide, for example, a gene modifying polypeptide and gene modifying template. In some embodiments, multicistronic expression constructs may exhibit reduced expression levels of one or more of the included transgenes, for example, because of promoter interference or the presence of incompatible nucleic acid elements in close proximity. If a multicistronic expression construct is part of a viral vector, the presence of a self-complementary nucleic acid sequence may, in some instances, interfere with the formation of structures necessary for viral reproduction or packaging.

In some embodiments, the sequence encodes an RNA with a hairpin. In some embodiments, the hairpin RNA is a guide RNA, a template RNA, a shRNA, or a microRNA, In some embodiments, the first promoter is an RNA polymerase I promoter. In some embodiments, the first promoter is an RNA polymerase II promoter. In some embodiments, the second promoter is an RNA polymerase 111 promoter. In some embodiments the second promoter is a U6 or H1 promoter.

Without wishing to be bound by theory, multicistronic expression constructs may not achieve optimal expression levels as compared to expression systems containing only one cistron. One of the suggested causes of lower expression levels achieved with multicistronic expression constructs comprising two or more promoter elements is the Phenomenon of promoter interference (see. e.g., Curtin J A, Dane A P, Swanson A, Alexander I E, Ginn S L. Bidirectional promoter interference between two widely used internal heterologous promoters in a late-generation lentiviral construct. Gene Ther. 2008 March; 15(5):384-90; and Martin-Duque P, Jezzard S, Kaftansis L, Vassaux G. Direct comparison of the insulating properties of two genetic elements in an adenoviral vector containing two different expression cassettes. Hum Gene Ther. 2004 October; 15(10):995-1002; both references incorporated herein by reference for disclosure of promoter interference phenomenon), In some embodiments, the problem of promoter interference may be overcome, e.g., by producing multicistronic expression constructs comprising only one promoter driving transcription of multiple encoding nucleic acid sequences separated by internal ribosomal entry, sites, or by separating cistrons comprising their own promoter with transcriptional insulator elements. In some embodiments, single-promoter driven expression of multiple cistrons may result in uneven expression levels of the cistrons. In some embodiments, a promoter cannot efficiently be isolated and isolation elements may not be compatible with some gene transfer vectors, for example, some retroviral vectors.

MicroRNAs

MicroRNAs (miRNAs) and other small interfering nucleic acids generally regulate gene expression via target RNA transcript cleavage/degradation or translational repression of the target messenger RNA (mRNA). miRNAs may, in some instances, be natively expressed, typically as final 19-25 non-translated RNA products. miRNAs generally exhibit their activity through sequence-specific interactions with the 3′ untranslated regions (UTR) of target mRNAs. These endogenously expressed miRNAs may form hairpin precursors that are subsequently processed into an miRNA duplex, and further into a mature single stranded miRNA molecule. This mature miRNA generally guides a multiprotein complex, miRISC, which identifies target 3′ UTR regions of target mRNAs based upon their complementarity to the mature miRNA. Useful transgene products may include, for example, miRNAs or miRNA binding sites that regulate the expression of a linked polypeptide. A non-limiting list of miRNA genes; the products of these genes and their homologues are useful as transgenes or as targets for small interfering nucleic acids (e.g., miRNA sponges, antisense oligonucleotides), e.g. in methods such as those listed in U.S. Ser. No. 10/300,146, 22:25-25:48, are herein incorporated by reference. In some embodiments, one or more binding sites for one or more of the foregoing miRNA s are incorporated in a transgene, e.g., a transgene delivered by a rAAV vector, e.g., to inhibit the expression of the transgene in one or more tissues of an animal harboring the transgene. In some embodiments, a binding site may be selected to control the expression of a transgene in a tissue specific manner. For example, binding sites for the liver-specific miR-122 may be incorporated into a transgene to inhibit expression of that transgene in the liver. Additional exemplary miRNA sequences are described, for example, in U.S. Pat. No. 10,300,146 (incorporated herein by reference in its entirety).

An miR inhibitor or miRNA inhibitor is generally an agent that blocks miRNA expression and/or processing. Examples of such agents include, but are not limited to, microRNA antagonists, microRNA specific antisense, microRNA sponges, and microRNA oligonucleotides (double-stranded, hairpin, short oligonucleotides) that inhibit miRNA interaction with a Drosha complex. MicroRNA inhibitors, e.g., miRNA sponges, can be expressed in cells from transgenes (e.g., as described in Ebert M. S. Nature Methods. Epub Aug. 12, 2007; incorporated by reference herein in its entirety). In some embodiments, microRNA sponges, or other miR inhibitors, are used with the AAVs. microRNA sponges generally specifically inhibit miRNAs through a complementary heptameric seed sequence. In some embodiments, an entire family of miRNAs can be silenced using a single sponge sequence. Other methods for silencing miRNA function (derepression of miRNA targets) in cells will be apparent to one of ordinary skill in the art.

In some embodiments, a gene modifying system, template RNA, or polypeptide described herein is administered to or is active in (e.g., is more active in) a target tissue, e.g., a first tissue. In some embodiments, the gene modifying system, template RNA, or polypeptide is not administered to or is less active in (e.g., not active in) a non-target tissue. In some embodiments, a gene modifying system, template RNA, or polypeptide described herein is useful for modifying DNA in a target tissue, e.g., a first tissue, (e.g., and not modifying DNA in a non-target tissue).

In some embodiments, a gene modifying system comprises (a) a polypeptide described herein or a nucleic acid encoding the same, (b) a template nucleic acid (e.g., template RNA) described herein, and (c) one or more first tissue-specific expression-control sequences specific to the target tissue, wherein the one or more first tissue-specific expression-control sequences specific to the target tissue are in operative association with (a), (b), or (a) and (b), wherein, when associated with (a), (a) comprises a nucleic acid encoding the polypeptide.

In some embodiments, the nucleic acid in (b) comprises RNA.

In some embodiments, the nucleic acid in (b) comprises DNA.

In some embodiments, the nucleic acid in (b): (i) is single-stranded or comprises a single-stranded segment, e.g., is single-stranded DNA or comprises a single-stranded segment and one or more double stranded segments; (ii) has inverted terminal repeats; or (iii) both (i) and (ii).

In some embodiments, the nucleic acid in (b) is double-stranded or comprises a double-stranded segment.

In some embodiments, (a) comprises a nucleic acid encoding the polypeptide.

In some embodiments, the nucleic acid in (a) comprises RNA.

In some embodiments, the nucleic acid in (a) comprises DNA.

In some embodiments, the nucleic acid in (a): (i) is single-stranded or comprises a single-stranded segment, e.g., is single-stranded DNA or comprises a single-stranded segment and one or more double stranded segments; (ii) has inverted terminal repeats; or (iii) both (i) and (ii).

In some embodiments, the nucleic acid in (a) is double-stranded or comprises a double-stranded segment.

In some embodiments, the nucleic acid in (a), (b), or (a) and (b) is linear.

In some embodiments, the nucleic acid in (a), (b), or (a) and (b) is circular, e.g., a plasmid or minicircle.

In some embodiments, the heterologous object sequence is in operative association with a first promoter.

In some embodiments, the one or more first tissue-specific expression-control sequences comprises a tissue specific promoter.

In some embodiments, the tissue-specific promoter comprises a first promoter in operative association with: (i) the heterologous object sequence, (ii) a nucleic acid encoding the retroviral RT, or (iii) (i) and (ii).

In some embodiments, the one or more first tissue-specific expression-control sequences comprises a tissue-specific microRNA recognition sequence in operative association with: (i) the heterologous object sequence, (ii) a nucleic acid encoding the retroviral RT domain, or (iii) (i) and (ii).

In some embodiments, a system comprises a tissue-specific promoter, and the system further comprises one or more tissue-specific microRNA recognition sequences, wherein: (i) the tissue specific promoter is in operative association with: (I) the heterologous object sequence, (II) a nucleic acid encoding the retroviral RT domain, or (III) (I) and (II); and/or (ii) the one or more tissue-specific microRNA recognition sequences are in operative association with: (I) the heterologous object sequence, (II) a nucleic acid encoding the retroviral RT, or (III) (I) and (II).

In some embodiments, wherein (a) comprises a nucleic acid encoding the polypeptide, the nucleic acid comprises a promoter in operative association with the nucleic acid encoding the polypeptide.

In some embodiments, the nucleic acid encoding the polypeptide comprises one or more second tissue-specific expression-control sequences specific to the target tissue in operative association with the polypeptide coding sequence.

In some embodiments, the one or more second tissue-specific expression-control sequences comprises a tissue specific promoter.

In some embodiments, the tissue-specific promoter is the promoter in operative association with the nucleic acid encoding the polypeptide.

In some embodiments, the one or more second tissue-specific expression-control sequences comprises a tissue-specific microRNA recognition sequence.

In some embodiments, the promoter in operative association with the nucleic acid encoding the polypeptide is a tissue-specific promoter, the system further comprising one or more tissue-specific microRNA recognition sequences.

In some embodiments, a nucleic acid component of a system provided by the invention is a sequence (e.g., encoding the polypeptide or comprising a heterologous object sequence) flanked by untranslated regions (UTRs) that modify protein expression levels. Various 5′ and 3′ UTRs can affect protein expression. For example, in some embodiments, the coding sequence may be preceded by a 5′ UTR that modifies RNA stability or protein translation. In some embodiments, the sequence may be followed by a 3′ UTR that modifies RNA stability or translation. In some embodiments, the sequence may be preceded by a 5′ UTR and followed by a 3′ UTR that modify RNA stability or translation. In some embodiments, the 5′ and/or 3′ UTR may be selected from the 5′ and 3′ UTRs of complement factor 3 (C3) (CACTCCTCCCCATCCTCTCCCTCTGTCCCTCTGTCCCTCTGACCCTGCACTGTCCCAGCACC; SEQ ID NO: 11,004) or orosomucoid 1 (ORM1) (CAGGACACAGCCTTGGATCAGGACAGAGACTTGGGGGCCATCCTGCCCCTCCAACCCGACA TGTGTACCTCAGCTTTTTCCCTCACTTGCATCAATAAAGCTTCTGTGTTTGGAACAGCTAA; SEQ ID NO: 11,005) (Asrani et al. RNA Biology 2018). In certain embodiments, the 5′ UTR is the 5′ UTR from C3 and the 3′ UTR is the 3′ UTR from ORM1. In certain embodiments, a 5′ UTR and 3′ UTR for protein expression, e.g., mRNA (or DNA encoding the RNA) for a gene modifying polypeptide or heterologous object sequence, comprise optimized expression sequences. In some embodiments, the 5′ UTR comprises GGGAAAUAAGAGAGAAAAGAAGAGUAAGAAGAAAUAUAAGAGCCACC (SEQ ID NO: 11,006) and/or the 3′ UTR comprising UGAUAAUAGGCUGGAGCCUCGGUGGCCAUGCUUCUUGCCCCUUGGGCCUCCCCCCAGCCC CUCCUCCCCUUCCUGCACCCGUACCCCCGUGGUCUUUGAAUAAAGUCUGA (SEQ ID NO: 11,007), e.g., as described in Richner et al. Cell 168(6): P1114-1125 (2017), the sequences of which are incorporated herein by reference.

In some embodiments, a 5′ and/or 3′ UTR may be selected to enhance protein expression. In some embodiments, a 5′ and/or 3′ UTR may be selected to modify protein expression such that overproduction inhibition is minimized. In some embodiments, UTRs are around a coding sequence, e.g., outside the coding sequence and in other embodiments proximal to the coding sequence. In some embodiments, additional regulatory elements (e.g., miRNA binding sites, cis-regulatory sites) are included in the UTRs.

In some embodiments, an open reading frame of a gene modifying system, e.g., an ORF of an mRNA (or DNA encoding an mRNA) encoding a gene modifying polypeptide or one or more ORFs of an mRNA (or DNA encoding an mRNA) of a heterologous object sequence, is flanked by a 5′ and/or 3′ untranslated region (UTR) that enhances the expression thereof. In some embodiments, the 5′ UTR of an mRNA component (or transcript produced from a DNA component) of the system comprises the sequence 5′-GGGAAAUAAGAGAGAAAAGAAGAGUAAGAAGAAAUAUAAGAGCCACC-3′; SEQ ID NO: 11,008). In some embodiments, the 3′ UTR of an mRNA component (or transcript produced from a DNA component) of the system comprises the sequence 5′-UGAUAAUAGGCUGGAGCCUCGGUGGCCAUGCUUCUUGCCCCUUGGGCCUCCCCCCAGCCC CUCCUCCCCUUCCUGCACCCGUACCCCCGUGGUCUUUGAAUAAAGUCUGA-3′ (SEQ ID NO: 11,009). This combination of 5′ UTR and 3′ UTR has been shown to result in desirable expression of an operably linked ORF by Richner et al. Cell 168(6): P1114-1125 (2017), the teachings and sequences of which are incorporated herein by reference. In some embodiments, a system described herein comprises a DNA encoding a transcript, wherein the DNA comprises the corresponding 5′ UTR and 3′ UTR sequences, with T substituting for U in the above-listed sequence). In some embodiments, a DNA vector used to produce an RNA component of the system further comprises a promoter upstream of the 5′ UTR for initiating in vitro transcription, e.g, a T7, T3, or SP6 promoter. The 5′ UTR above begins with GGG, which is a suitable start for optimizing transcription using T7 RNA polymerase. For tuning transcription levels and altering the transcription start site nucleotides to fit alternative 5′ UTRs, the teachings of Davidson et al. Pac Symp Biocomput 433-443 (2010) describe T7 promoter variants, and the methods of discovery thereof, that fulfill both of these traits.

Viral Vectors and Components Thereof

Viruses are a useful source of delivery vehicles for the systems described herein, in addition to a source of relevant enzymes or domains as described herein, e.g., as sources of polymerases and polymerase functions used herein, e.g., DNA-dependent DNA polymerase, RNA-dependent RNA polymerase, RNA-dependent DNA polymerase, DNA-dependent RNA polymerase, reverse transcriptase. Some enzymes, e.g., reverse transcriptases, may have multiple activities, e.g., be capable of both RNA-dependent DNA polymerization and DNA-dependent DNA polymerization, e.g., first and second strand synthesis. In some embodiments, the virus used as a gene modifying delivery system or a source of components thereof may be selected from a group as described by Baltimore Bacteriol Rev 35(3):235-241 (1971).

In some embodiments, the virus is selected from a Group I virus, e.g., is a DNA virus and packages dsDNA into virions. In some embodiments, the Group I virus is selected from, e.g., Adenoviruses, Herpesviruses, Poxviruses.

In some embodiments, the virus is selected from a Group II virus, e.g., is a DNA virus and packages ssDNA into virions. In some embodiments, the Group II virus is selected from, e.g., Parvoviruses. In some embodiments, the parvovirus is a dependoparvovirus, e.g., an adeno-associated virus (AAV).

In some embodiments, the virus is selected from a Group III virus, e.g., is an RNA virus and packages dsRNA into virions. In some embodiments, the Group III virus is selected from, e.g., Reoviruses. In some embodiments, one or both strands of the dsRNA contained in such virions is a coding molecule able to serve directly as mRNA upon transduction into a host cell, e.g., can be directly translated into protein upon transduction into a host cell without requiring any intervening nucleic acid replication or polymerization steps.

In some embodiments, the virus is selected from a Group IV virus, e.g., is an RNA virus and packages ssRNA(+) into virions. In some embodiments, the Group IV virus is selected from, e.g., Coronaviruses, Picomaviruses, Togaviruses. In some embodiments, the ssRNA(+) contained in such virions is a coding molecule able to serve directly as mRNA upon transduction into a host cell, e.g., can be directly translated into protein upon transduction into a host cell without requiring any intervening nucleic acid replication or polymerization steps.

In some embodiments, the virus is selected from a Group V virus, e.g., is an RNA virus and packages ssRNA(−) into virions. In some embodiments, the Group V virus is selected from, e.g., Orthomyxoviruses, Rhabdoviruses. In some embodiments, an RNA virus with an ssRNA(−) genome also carries an enzyme inside the virion that is transduced to host cells with the viral genome, e.g., an RNA-dependent RNA polymerase, capable of copying the ssRNA(−) into ssRNA(+) that can be translated directly by the host.

In some embodiments, the virus is selected from a Group VI virus, e.g., is a retrovirus and packages ssRNA(+) into virions. In some embodiments, the Group VI virus is selected from, e.g., retroviruses. In some embodiments, the retrovirus is a lentivirus, e.g., HIV-1, HIV-2, SIV, BIV. In some embodiments, the retrovirus is a spumavirus, e.g., a foamy virus, e.g., HFV, SFV, BFV. In some embodiments, the ssRNA(+) contained in such virions is a coding molecule able to serve directly as mRNA upon transduction into a host cell, e.g., can be directly translated into protein upon transduction into a host cell without requiring any intervening nucleic acid replication or polymerization steps. In some embodiments, the ssRNA(+) is first reverse transcribed and copied to generate a dsDNA genome intermediate from which mRNA can be transcribed in the host cell. In some embodiments, an RNA virus with an ssRNA(+) genome also carries an enzyme inside the virion that is transduced to host cells with the viral genome, e.g., an RNA-dependent DNA polymerase, capable of copying the ssRNA(+) into dsDNA that can be transcribed into mRNA and translated by the host. In some embodiments, the reverse transcriptase from a Group VI retrovirus is incorporated as the reverse transcriptase domain of a gene modifying polypeptide.

In some embodiments, the virus is selected from a Group VII virus, e.g., is a retrovirus and packages dsRNA into virions. In some embodiments, the Group VII virus is selected from, e.g., Hepadnaviruses. In some embodiments, one or both strands of the dsRNA contained in such virions is a coding molecule able to serve directly as mRNA upon transduction into a host cell, e.g., can be directly translated into protein upon transduction into a host cell without requiring any intervening nucleic acid replication or polymerization steps. In some embodiments, one or both strands of the dsRNA contained in such virions is first reverse transcribed and copied to generate a dsDNA genome intermediate from which mRNA can be transcribed in the host cell. In some embodiments, an RNA virus with a dsRNA genome also carries an enzyme inside the virion that is transduced to host cells with the viral genome, e.g., an RNA-dependent DNA polymerase, capable of copying the dsRNA into dsDNA that can be transcribed into mRNA and translated by the host. In some embodiments, the reverse transcriptase from a Group VII retrovirus is incorporated as the reverse transcriptase domain of a gene modifying polypeptide.

In some embodiments, virions used to deliver nucleic acid in this invention may also carry enzymes involved in the process of gene modification. For example, a retroviral virion may contain a reverse transcriptase domain that is delivered into a host cell along with the nucleic acid. In some embodiments, an RNA template may be associated with a gene modifying polypeptide within a virion, such that both are co-delivered to a target cell upon transduction of the nucleic acid from the viral particle. In some embodiments, the nucleic acid in a virion may comprise DNA, e.g., linear ssDNA, linear dsDNA, circular ssDNA, circular dsDNA, minicircle DNA, dbDNA, ceDNA. In some embodiments, the nucleic acid in a virion may comprise RNA, e.g., linear ssRNA, linear dsRNA, circular ssRNA, circular dsRNA. In some embodiments, a viral genome may circularize upon transduction into a host cell, e.g., a linear ssRNA molecule may undergo a covalent linkage to form a circular ssRNA, a linear dsRNA molecule may undergo a covalent linkage to form a circular dsRNA or one or more circular ssRNA. In some embodiments, a viral genome may replicate by rolling circle replication in a host cell. In some embodiments, a viral genome may comprise a single nucleic acid molecule, e.g., comprise a non-segmented genome. In some embodiments, a viral genome may comprise two or more nucleic acid molecules, e.g., comprise a segmented genome. In some embodiments, a nucleic acid in a virion may be associated with one or proteins. In some embodiments, one or more proteins in a virion may be delivered to a host cell upon transduction. In some embodiments, a natural virus may be adapted for nucleic acid delivery by the addition of virion packaging signals to the target nucleic acid, wherein a host cell is used to package the target nucleic acid containing the packaging signals.

In some embodiments, a virion used as a delivery vehicle may comprise a commensal human virus. In some embodiments, a virion used as a delivery vehicle may comprise an anellovirus, the use of which is described in WO2018232017A1, which is incorporated herein by reference in its entirety.

AAV Administration

In some embodiments, an adeno-associated virus (AAV) is used in conjunction with the system, template nucleic acid, and/or polypeptide described herein. In some embodiments, an AAV is used to deliver, administer, or package the system, template nucleic acid, and/or polypeptide described herein. In some embodiments, the AAV is a recombinant AAV (rAAV).

In some embodiments, a system comprises (a) a polypeptide described herein or a nucleic acid encoding the same, (b) a template nucleic acid (e.g., template RNA) described herein, and (c) one or more first tissue-specific expression-control sequences specific to the target tissue, wherein the one or more first tissue-specific expression-control sequences specific to the target tissue are in operative association with (a), (b), or (a) and (b), wherein, when associated with (a), (a) comprises a nucleic acid encoding the polypeptide.

In some embodiments, a system described herein further comprises a first recombinant adeno-associated virus (rAAV) capsid protein; wherein the at least one of (a) or (b) is associated with the first rAAV capsid protein, wherein at least one of (a) or (b) is flanked by AAV inverted terminal repeats (ITRs).

In some embodiments, (a) and (b) are associated with the first rAAV capsid protein.

In some embodiments, (a) and (b) are on a single nucleic acid.

In some embodiments, the system further comprises a second rAAV capsid protein, wherein at least one of (a) or (b) is associated with the second rAAV capsid protein, and wherein the at least one of (a) or (b) associated with the second rAAV capsid protein is different from the at least one of (a) or (b) is associated with the first rAAV capsid protein.

In some embodiments, the at least one of (a) or (b) is associated with the first or second rAAV capsid protein is dispersed in the interior of the first or second rAAV capsid protein, which first or second rAAV capsid protein is in the form of an AAV capsid particle.

In some embodiments, the system further comprises a nanoparticle, wherein the nanoparticle is associated with at least one of (a) or (b).

In some embodiments, (a) and (b), respectively are associated with: a) a first rAAV capsid protein and a second rAAV capsid protein; b) a nanoparticle and a first rAAV capsid protein; c) a first rAAV capsid protein; d) a first adenovirus capsid protein; e) a first nanoparticle and a second nanoparticle; or f) a first nanoparticle.

Viral vectors are useful for delivering all or part of a system provided by the invention, e.g., for use in methods provided by the invention. Systems derived from different viruses have been employed for the delivery of polypeptides or nucleic acids; for example: integrase-deficient lentivirus, adenovirus, adeno-associated virus (AAV), herpes simplex virus, and baculovirus (reviewed in Hodge et al. Hum Gene Ther 2017; Narayanavari et al. Crit Rev Biochem Mol Biol 2017; Boehme et al. Curr Gene Ther 2015).

Adenoviruses are common viruses that have been used as gene delivery vehicles given well-defined biology, genetic stability, high transduction efficiency, and ease of large-scale production (see, for example, review by Lee et al. Genes & Diseases 2017). They possess linear dsDNA genomes and come in a variety of serotypes that differ in tissue and cell tropisms. In order to prevent replication of infectious virus in recipient cells, adenovirus genomes used for packaging are deleted of some or all endogenous viral proteins, which are provided in trans in viral production cells. This renders the genomes helper-dependent, meaning they can only be replicated and packaged into viral particles in the presence of the missing components provided by so-called helper functions. A helper-dependent adenovirus system with all viral ORFs removed may be compatible with packaging foreign DNA of up to ˜37 kb (Parks et al. J Virol 1997). In some embodiments, an adenoviral vector is used to deliver DNA corresponding to the polypeptide or template component of the gene modifying system, or both are contained on separate or the same adenoviral vector. In some embodiments, the adenovirus is a helper-dependent adenovirus (HD-AdV) that is incapable of self-packaging. In some embodiments, the adenovirus is a high-capacity adenovirus (HC-AdV) that has had all or a substantial portion of endogenous viral ORFs deleted, while retaining the necessary sequence components for packaging into adenoviral particles. For this type of vector, the only adenoviral sequences required for genome packaging are noncoding sequences: the inverted terminal repeats (ITRs) at both ends and the packaging signal at the 5′-end (Jager et al. Nat Protoc 2009). In some embodiments, the adenoviral genome also comprises stuffer DNA to meet a minimal genome size for optimal production and stability (see, for example, Hausl et al. Mol Ther 2010). In some embodiments, an adenovirus is used to deliver a gene modifying system to the liver.

In some embodiments, an adenovirus is used to deliver a gene modifying system to HSCs, e.g., HDAd5/35++. HDAd5/35++ is an adenovirus with modified serotype 35 fibers that de-target the vector from the liver (Wang et al. Blood Adv 2019). In some embodiments, the adenovirus that delivers a gene modifying system to HSCs utilizes a receptor that is expressed specifically on primitive HSCs, e.g., CD46.

Adeno-associated viruses (AAV) belong to the parvoviridae family and more specifically constitute the dependoparvovirus genus. The AAV genome is composed of a linear single-stranded DNA molecule which contains approximately 4.7 kilobases (kb) and consists of two major open reading frames (ORFs) encoding the non-structural Rep (replication) and structural Cap (capsid) proteins. A second ORF within the cap gene was identified that encodes the assembly-activating protein (AAP). The DNAs flanking the AAV coding regions are two cis-acting inverted terminal repeat (ITR) sequences, approximately 145 nucleotides in length, with interrupted palindromic sequences that can be folded into energetically stable hairpin structures that function as primers of DNA replication. In addition to their role in DNA replication, the ITR sequences have been shown to be involved in viral DNA integration into the cellular genome, rescue from the host genome or plasmid, and encapsidation of viral nucleic acid into mature virions (Muzyczka, (1992) Curr. Top. Micro. Immunol. 158:97-129). In some embodiments, one or more gene modifying nucleic acid components is flanked by ITRs derived from AAV for viral packaging. See, e.g., WO2019113310.

In some embodiments, one or more components of the gene modifying system are carried via at least one AAV vector. In some embodiments, the at least one AAV vector is selected for tropism to a particular cell, tissue, organism. In some embodiments, the AAV vector is pseudotyped, e.g., AAV2/8, wherein AAV2 describes the design of the construct but the capsid protein is replaced by that from AAV8. It is understood that any of the described vectors could be pseudotype derivatives, wherein the capsid protein used to package the AAV genome is derived from that of a different AAV serotype. Without wishing to be limited in vector choice, a list of exemplary AAV serotypes can be found in Table 18. In some embodiments, an AAV to be employed for gene modifying may be evolved for novel cell or tissue tropism as has been demonstrated in the literature (e.g., Davidsson et al. Proc Natl Acad Sci USA 2019).

In some embodiments, the AAV delivery vector is a vector which has two AAV inverted terminal repeats (ITRs) and a nucleotide sequence of interest (for example, a sequence coding for a gene modifying polypeptide or a DNA template, or both), each of said ITRs having an interrupted (or noncontiguous) palindromic sequence, i.e., a sequence composed of three segments: a first segment and a last segment that are identical when read 5′→3′ but hybridize when placed against each other, and a segment that is different that separates the identical segments. See, for example, WO2012123430.

Conventionally, AAV virions with capsids are produced by introducing a plasmid or plasmids encoding the rAAV or scAAV genome, Rep proteins, and Cap proteins (Grimm et al, 1998). Upon introduction of these helper plasmids in trans, the AAV genome is “rescued” (i.e., released and subsequently recovered) from the host genome, and is further encapsidated to produce infectious AAV. In some embodiments, one or more gene modifying nucleic acids are packaged into AAV particles by introducing the ITR-flanked nucleic acids into a packaging cell in conjunction with the helper functions.

In some embodiments, the AAV genome is a so called self-complementary genome (referred to as scAAV), such that the sequence located between the ITRs contains both the desired nucleic acid sequence (e.g., DNA encoding the gene modifying polypeptide or template, or both) in addition to the reverse complement of the desired nucleic acid sequence, such that these two components can fold over and self-hybridize. In some embodiments, the self-complementary modules are separated by an intervening sequence that permits the DNA to fold back on itself, e.g., forms a stem-loop. An scAAV has the advantage of being poised for transcription upon entering the nucleus, rather than being first dependent on ITR priming and second-strand synthesis to form dsDNA. In some embodiments, one or more gene modifying components is designed as an scAAV, wherein the sequence between the AAV ITRs contains two reverse complementing modules that can self-hybridize to create dsDNA.

In some embodiments, nucleic acid (e.g., encoding a polypeptide, or a template, or both) delivered to cells is closed-ended, linear duplex DNA (CELiD DNA or ceDNA). In some embodiments, ceDNA is derived from the replicative form of the AAV genome (Li et al. PLoS One 2013). In some embodiments, the nucleic acid (e.g., encoding a polypeptide, or a template DNA, or both) is flanked by ITRs, e.g., AAV ITRs, wherein at least one of the ITRs comprises a terminal resolution site and a replication protein binding site (sometimes referred to as a replicative protein binding site). In some embodiments, the ITRs are derived from an adeno-associated virus, e.g., AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV10, AAV11, AAV12, or a combination thereof. In some embodiments, the ITRs are symmetric. In some embodiments, the ITRs are asymmetric. In some embodiments, at least one Rep protein is provided to enable replication of the construct. In some embodiments, the at least one Rep protein is derived from an adeno-associated virus, e.g., AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV10, AAV11, AAV12, or a combination thereof. In some embodiments, ceDNA is generated by providing a production cell with (i) DNA flanked by ITRs, e.g., AAV ITRs, and (ii) components required for ITR-dependent replication, e.g., AAV proteins Rep78 and Rep52 (or nucleic acid encoding the proteins). In some embodiments, ceDNA is free of any capsid protein, e.g., is not packaged into an infectious AAV particle. In some embodiments, ceDNA is formulated into LNPs (see, for example, WO2019051289A1).

In some embodiments, the ceDNA vector consists of two self-complementary sequences, e.g., asymmetrical or symmetrical or substantially symmetrical ITRs as defined herein, flanking said expression cassette, wherein the ceDNA vector is not associated with a capsid protein. In some embodiments, the ceDNA vector comprises two self-complementary sequences found in an AAV genome, where at least one ITR comprises an operative Rep-binding element (RBE) (also sometimes referred to herein as “RBS”) and a terminal resolution site (trs) of AAV or a functional variant of the RBE. See, for example, WO2019113310.

In some embodiments, the AAV genome comprises two genes that encode four replication proteins and three capsid proteins, respectively. In some embodiments, the genes are flanked on either side by 145-bp inverted terminal repeats (ITRs). In some embodiments, the virion comprises up to three capsid proteins (Vp1, Vp2, and/or Vp3), e.g., produced in a 1:1:10 ratio. In some embodiments, the capsid proteins are produced from the same open reading frame and/or from differential splicing (Vp1) and alternative translational start sites (Vp2 and Vp3, respectively). Generally, Vp3 is the most abundant subunit in the virion and participates in receptor recognition at the cell surface defining the tropism of the virus. In some embodiments, Vp1 comprises a phospholipase domain, e.g., which functions in viral infectivity, in the N-terminus of Vp1.

In some embodiments, packaging capacity of the viral vectors limits the size of the gene modifying system that can be packaged into the vector. For example, the packaging capacity of the AAVs can be about 4.5 kb (e.g., about 3.0, 3.5, 4.0, 4.5, 5.0, 5.5, or 6.0 kb), e.g., including one or two inverted terminal repeats (ITRs), e.g., 145 base ITRs.

In some embodiments, recombinant AAV (rAAV) comprises cis-acting 145-bp ITRs flanking vector transgene cassettes, e.g., providing up to 4.5 kb for packaging of foreign DNA. Subsequent to infection, rAAV can, in some instances, express a fusion protein of the invention and persist without integration into the host genome by existing episomally in circular head-to-tail concatemers. rAAV can be used, for example, in vitro and in vivo. In some embodiments, AAV-mediated gene delivery requires that the length of the coding sequence of the gene is equal or greater in size than the wild-type AAV genome.

AAV delivery of genes that exceed this size and/or the use of large physiological regulatory elements can be accomplished, for example, by dividing the protein(s) to be delivered into two or more fragments. In some embodiments, the N-terminal fragment is fused to an intein-N sequence. In some embodiments, the C-terminal fragment is fused to an intein-C sequence. In embodiments, the fragments are packaged into two or more AAV vectors.

In some embodiments, dual AAV vectors are generated by splitting a large transgene expression cassette in two separate halves (5′ and 3′ ends, or head and tail), e.g., wherein each half of the cassette is packaged in a single AAV vector (of <5 kb). The re-assembly of the full-length transgene expression cassette can, in some embodiments, then be achieved upon co-infection of the same cell by both dual AAV vectors. In some embodiments, co-infection is followed by one or more of: (1) homologous recombination (HR) between 5′ and 3′ genomes (dual AAV overlapping vectors); (2) ITR-mediated tail-to-head concatemerization of 5′ and 3′ genomes (dual AAV trans-splicing vectors); and/or (3) a combination of these two mechanisms (dual AAV hybrid vectors). In some embodiments, the use of dual AAV vectors in vivo results in the expression of full-length proteins. In some embodiments, the use of the dual AAV vector platform represents an efficient and viable gene transfer strategy for transgenes of greater than about 4.0, 4.1, 4.2, 4.3, 4.4, 4.5, 4.6, 4.7, 4.8, 4.9, or 5.0 kb in size. In some embodiments, AAV vectors can also be used to transduce cells with target nucleic acids, e.g., in the in vitro production of nucleic acids and peptides. In some embodiments, AAV vectors can be used for in vivo and ex vivo gene therapy procedures (see, e.g., West et al., Virology 160:38-47 (1987); U.S. Pat. No. 4,797,368; WO 93/24641; Kotin, Human Gene Therapy 5:793-801 (1994); Muzyczka, J. Clin. Invest. 94:1351 (1994); each of which is incorporated herein by reference in their entirety). The construction of recombinant AAV vectors is described in a number of publications, including U.S. Pat. No. 5,173,414; Tratschin et al., Mol. Cell. Biol. 5:3251-3260 (1985); Tratschin, et al., Mol. Cell. Biol. 4:2072-2081 (1984); Hermonat & Muzyczka, PNAS 81:6466-6470 (1984); and Samulski et al., J. Virol. 63:03822-3828 (1989) (incorporated by reference herein in their entirety).

In some embodiments, a gene modifying polypeptide described herein (e.g., with or without one or more guide nucleic acids) can be delivered using AAV, lentivirus, adenovirus or other plasmid or viral vector types, in particular, using formulations and doses from, for example, U.S. Pat. No. 8,454,972 (formulations, doses for adenovirus), U.S. Pat. No. 8,404,658 (formulations, doses for AAV) and U.S. Pat. No. 5,846,946 (formulations, doses for DNA plasmids) and from clinical trials and publications regarding the clinical trials involving lentivirus, AAV and adenovirus. For example, for AAV, the route of administration, formulation and dose can be as described in U.S. Pat. No. 8,454,972 and as in clinical trials involving AAV. For adenovirus, the route of administration, formulation and dose can be as described in U.S. Pat. No. 8,404,658 and as in clinical trials involving adenovirus. For plasmid delivery, the route of administration, formulation and dose can be as described in U.S. Pat. No. 5,846,946 and as in clinical studies involving plasmids. Doses can be based on or extrapolated to an average 70 kg individual (e.g. a male adult human), and can be adjusted for patients, subjects, mammals of different weight and species. Frequency of administration is within the ambit of the medical or veterinary practitioner (e.g., physician, veterinarian), depending on usual factors including the age, sex, general health, other conditions of the patient or subject and the particular condition or symptoms being addressed. In some embodiments, the viral vectors can be injected into the tissue of interest. For cell-type specific gene modifying, the expression of the gene modifying polypeptide and optional guide nucleic acid can, in some embodiments, be driven by a cell-type specific promoter.

In some embodiments, AAV allows for low toxicity, for example, due to the purification method not requiring ultracentrifugation of cell particles that can activate the immune response. In some embodiments, AAV allows low probability of causing insertional mutagenesis, for example, because it does not substantially integrate into the host genome.

In some embodiments, AAV has a packaging limit of about 4.4, 4.5, 4.6, 4.7, or 4.75 kb. In some embodiments, a gene modifying polypeptide-encoding sequence, promoter, and transcription terminator can fit into a single viral vector. SpCas9 (4.1 kb) may, in some instances, be difficult to package into AAV. Therefore, in some embodiments, a gene modifying polypeptide coding sequence is used that is shorter in length than other gene modifying polypeptide coding sequences or base editors. In some embodiments, the gene modifying polypeptide encoding sequences are less than about 4.5 kb, 4.4 kb, 4.3 kb, 4.2 kb, 4.1 kb, 4 kb, 3.9 kb, 3.8 kb, 3.7 kb, 3.6 kb, 3.5 kb, 3.4 kb, 3.3 kb, 3.2 kb, 3.1 kb, 3 kb, 2.9 kb, 2.8 kb, 2.7 kb, 2.6 kb, 2.5 kb, 2 kb, or 1.5 kb.

An AAV can be AAV1, AAV2, AAV5 or any combination thereof. In some embodiments, the type of AAV is selected with respect to the cells to be targeted; e.g., AAV serotypes 1, 2, 5 or a hybrid capsid AAV1, AAV2, AAV5 or any combination thereof can be selected for targeting brain or neuronal cells; or AAV4 can be selected for targeting cardiac tissue. In some embodiments, AAV8 is selected for delivery to the liver. Exemplary AAV serotypes as to these cells are described, for example, in Grimm, D. et al, J. Virol. 82: 5887-5911 (2008) (incorporated herein by reference in its entirety). In some embodiments, AAV refers all serotypes, subtypes, and naturally-occurring AAV as well as recombinant AAV. AAV may be used to refer to the virus itself or a derivative thereof. In some embodiments, AAV includes AAV1, AAV2, AAV3, AAV3B, AAV4, AAV5, AAV6, AAV6.2, AAV7, AAVrh.64R1, AAVhu.37, AAVrh.8, AAVrh.32.33, AAV8, AAV9, AAV-DJ, AAV2/8, AAVrhlO, AAVLK03, AV10, AAV11, AAV12, rhlO, and hybrids thereof, avian AAV, bovine AAV, canine AAV, equine AAV, primate AAV, non-primate AAV, and ovine AAV. The genomic sequences of various serotypes of AAV, as well as the sequences of the native terminal repeats (TRs), Rep proteins, and capsid subunits are known in the art. Such sequences may be found in the literature or in public databases such as GenBank. Additional exemplary AAV serotypes are listed in Table 18.

TABLE 18 Exemplary AAV serotypes. Target Tissue Vehicle Reference Liver AAV (AAV8¹, AAVrh.8¹, AAVhu.37¹, AAV2/8, 1. Wang et al., Mol. Ther. 18, 118-25 (2010) AAV2/rh10², AAV9, AAV2, NP40³, NP59^(2,3), 2. Ginn et al., JHEP Reports, 100065 (2019) AAV3B⁵, AAV-DJ⁴, AAV-LK01⁴, AAV-LK02⁴, AAV- 3. Paulk et al., Mol. Ther. 26, 289-303 (2018). LK03⁴, AAV-LK19⁴, AAV5⁷ Adenovirus (Ad5, HC-AdV6) 4. L. Lisowski et al., Nature. 506, 382-6 (2014). 5. L. Wang et al., Mol. Ther. 23, 1877-87 (2015). 6. Hausl Mol Ther (2010) 7. Davidoff et al., Mol. Ther. 11, 875-88 (2005) Lung AAV (AAV4, AAV5, AAV61, AAV9, H222) 1. Duncan et al., Mol Ther Methods Clin Dev (2018) Adenovirus (Ad5, Ad3, Ad21, Ad14)3 2. Cooney et al., Am J Respir Cell Mol Biol (2019) 3. Li et al., Mol Ther Methods Clin Dev (2019) Skin AAV (AAV61, AAV-LK192) 1. Petek et al., Mol. Ther. (2010) 2. L. Lisowski et al., Nature. 506, 382-6 (2014). HSCs Adenovirus (HDAd5/35++) Wang et al. Blood Adv (2019)

In some embodiments, a pharmaceutical composition (e.g., comprising an AAV as described herein) has less than 10% empty capsids, less than 8% empty capsids, less than 7% empty capsids, less than 5% empty capsids, less than 3% empty capsids, or less than 1% empty capsids. In some embodiments, the pharmaceutical composition has less than about 5% empty capsids. In some embodiments, the number of empty capsids is below the limit of detection. In some embodiments, it is advantageous for the pharmaceutical composition to have low amounts of empty capsids, e.g., because empty capsids may generate an adverse response (e.g., immune response, inflammatory response, liver response, and/or cardiac response), e.g., with little or no substantial therapeutic benefit.

In some embodiments, the residual host cell protein (rHCP) in the pharmaceutical composition is less than or equal to 100 ng/ml rHCP per 1×10¹³ vg/ml, e.g., less than or equal to 40 ng/ml rHCP per 1×10¹³ vg/ml or 1-50 ng/ml rHCP per 1×10¹³ vg/ml. In some embodiments, the pharmaceutical composition comprises less than 10 ng rHCP per 1.0×10¹³ vg, or less than 5 ng rHCP per 1.0×10¹³ vg, less than 4 ng rHCP per 1.0×10¹³ vg, or less than 3 ng rHCP per 1.0×10¹³ vg, or any concentration in between. In some embodiments, the residual host cell DNA (hcDNA) in the pharmaceutical composition less than or equal to 5×10⁶ pg/ml hcDNA per 1×10¹³ vg/ml, less than or equal to 1.2×10⁶ pg/ml hcDNA per 1×10¹³ vg/ml, or 1×10⁵ pg/ml hcDNA per 1×10¹³ vg/ml. In some embodiments, the residual host cell DNA in said pharmaceutical composition is less than 5.0×10⁵ pg per 1×10¹³ vg, less than 2.0×10⁵ pg per 1.0×10¹³ vg, less than 1.1×10⁵ pg per 1.0×10¹³ vg, less than 1.0×10⁵ pg hcDNA per 1.0×10¹³ vg, less than 0.9×10⁵ pg hcDNA per 1.0×10¹³ vg, less than 0.8×10⁵ pg hcDNA per 1.0×10¹³ vg, or any concentration in between.

In some embodiments, the residual plasmid DNA in the pharmaceutical composition is less than or equal to 1.7×10⁵ pg/ml per 1.0×10¹³ vg/ml, or 1×10⁵ pg/ml per 1×10×10¹³ vg/ml, or 1.7×10⁶ pg/ml per 1.0×10¹³ vg/ml. In some embodiments, the residual DNA plasmid in the pharmaceutical composition is less than 10.0×10⁵ pg by 1.0×10¹³ vg, less than 8.0×10⁵ pg by 1.0×10¹³ vg or less than 6.8×10⁵ pg by 1.0×10¹³ vg. In embodiments, the pharmaceutical composition comprises less than 0.5 ng per 1.0×10¹³ vg, less than 0.3 ng per 1.0×10¹³ vg, less than 0.22 ng per 1.0×10¹³ vg or less than 0.2 ng per 1.0×10¹³ vg or any intermediate concentration of bovine serum albumin (BSA). In embodiments, the benzonase in the pharmaceutical composition is less than 0.2 ng by 1.0×10¹³ vg, less than 0.1 ng by 1.0×10¹³ vg, less than 0.09 ng by 1.0×10¹³ vg, less than 0.08 ng by 1.0×10¹³ vg or any intermediate concentration. In embodiments, Poloxamer 188 in the pharmaceutical composition is about 10 to 150 ppm, about 15 to 100 ppm or about 20 to 80 ppm. In embodiments, the cesium in the pharmaceutical composition is less than 50 pg/g (ppm), less than 30 pg/g (ppm) or less than 20 pg/g (ppm) or any intermediate concentration.

In embodiments, the pharmaceutical composition comprises total impurities, e.g., as determined by SDS-PAGE, of less than 10%, less than 8%, less than 7%, less than 6%, less than 5%, less than 4%, less than 3%, less than 2%, or any percentage in between. In embodiments, the total purity, e.g., as determined by SDS-PAGE, is greater than 90%, greater than 92%, greater than 93%, greater than 94%, greater than 95%, greater than 96%, greater than 97%, greater than 98%, or any percentage in between. In embodiments, no single unnamed related impurity, e.g., as measured by SDS-PAGE, is greater than 5%, greater than 4%, greater than 3% or greater than 2%, or any percentage in between. In embodiments, the pharmaceutical composition comprises a percentage of filled capsids relative to total capsids (e.g., peak 1+peak 2 as measured by analytical ultracentrifugation) of greater than 85%, greater than 86%, greater than 87%, greater than 88%, greater than 89%, greater than 90%, greater than 91%, greater than 91.9%, greater than 92%, greater than 93%, or any percentage in between. In embodiments of the pharmaceutical composition, the percentage of filled capsids measured in peak 1 by analytical ultracentrifugation is 20-80%, 25-75%, 30-75%, 35-75%, or 37.4-70.3%. In embodiments of the pharmaceutical composition, the percentage of filled capsids measured in peak 2 by analytical ultracentrifugation is 20-80%, 20-70%, 22-65%, 24-62%, or 24.9-60.1%.

In one embodiment, the pharmaceutical composition comprises a genomic titer of 1.0 to 5.0×10¹³ vg/mL, 1.2 to 3.0×10¹³ vg/mL or 1.7 to 2.3×10¹³ vg/ml. In one embodiment, the pharmaceutical composition exhibits a biological load of less than 5 CFU/mL, less than 4 CFU/mL, less than 3 CFU/mL, less than 2 CFU/mL or less than 1 CFU/mL or any intermediate contraction. In embodiments, the amount of endotoxin according to USP, for example, USP<85> (incorporated by reference in its entirety) is less than 1.0 EU/mL, less than 0.8 EU/mL or less than 0.75 EU/mL. In embodiments, the osmolarity of a pharmaceutical composition according to USP, for example, USP<785> (incorporated by reference in its entirety) is 350 to 450 mOsm/kg, 370 to 440 mOsm/kg or 390 to 430 mOsm/kg. In embodiments, the pharmaceutical composition contains less than 1200 particles that are greater than 25 m per container, less than 1000 particles that are greater than 25 μm per container, less than 500 particles that are greater than 25 μm per container or any intermediate value. In embodiments, the pharmaceutical composition contains less than 10,000 particles that are greater than 10 m per container, less than 8000 particles that are greater than 10 μm per container or less than 600 particles that are greater than 10 pm per container.

In one embodiment, the pharmaceutical composition has a genomic titer of 0.5 to 5.0×10¹³ vg/mL, 1.0 to 4.0×10¹³ vg/mL, 1.5 to 3.0×10¹³ vg/ml or 1.7 to 2.3×10¹³ vg/ml. In one embodiment, the pharmaceutical composition described herein comprises one or more of the following: less than about 0.09 ng benzonase per 1.0×10¹³ vg, less than about 30 pg/g (ppm) of cesium, about 20 to 80 ppm Poloxamer 188, less than about 0.22 ng BSA per 1.0×10¹³ vg, less than about 6.8×10⁵ pg of residual DNA plasmid per 1.0×10¹³ vg, less than about 1.1×10⁵ pg of residual hcDNA per 1.0×10¹³ vg, less than about 4 ng of rHCP per 1.0×10¹³ vg, pH 7.7 to 8.3, about 390 to 430 mOsm/kg, less than about 600 particles that are >25 m in size per container, less than about 6000 particles that are >10 m in size per container, about 1.7×10¹³-2.3×10¹³ vg/mL genomic titer, infectious titer of about 3.9×10⁸ to 8.4×10¹⁰ IU per 1.0×10¹³ vg, total protein of about 100-300 pg per 1.0×10¹³ vg, mean survival of >24 days in A7SMA mice with about 7.5×10¹³ vg/kg dose of viral vector, about 70 to 130% relative potency based on an in vitro cell based assay and/or less than about 5% empty capsid. In various embodiments, the pharmaceutical compositions described herein comprise any of the viral particles discussed here, retain a potency of between ±20%, between ±15%, between ±10% or within ±5% of a reference standard. In some embodiments, potency is measured using a suitable in vitro cell assay or in vivo animal model.

Additional methods of preparation, characterization, and dosing AAV particles are taught in WO2019094253, which is incorporated herein by reference in its entirety.

Additional rAAV constructs that can be employed consonant with the invention include those described in Wang et al 2019, available at: doi.org/10.1038/s41573-019-0012-9, including Table 1 thereof, which is incorporated by reference in its entirety.

Lipid Nanoparticles

The methods and systems provided herein may employ any suitable carrier or delivery modality, including, in certain embodiments, lipid nanoparticles (LNPs). Lipid nanoparticles, in some embodiments, comprise one or more ionic lipids, such as non-cationic lipids (e.g., neutral or anionic, or zwitterionic lipids); one or more conjugated lipids (such as PEG-conjugated lipids or lipids conjugated to polymers described in Table 5 of WO2019217941; incorporated herein by reference in its entirety); one or more sterols (e.g., cholesterol); and, optionally, one or more targeting molecules (e.g., conjugated receptors, receptor ligands, antibodies); or combinations of the foregoing.

Lipids that can be used in nanoparticle formations (e.g., lipid nanoparticles) include, for example those described in Table 4 of WO2019217941, which is incorporated by reference—e.g., a lipid-containing nanoparticle can comprise one or more of the lipids in Table 4 of WO2019217941. Lipid nanoparticles can include additional elements, such as polymers, such as the polymers described in Table 5 of WO2019217941, incorporated by reference.

In some embodiments, conjugated lipids, when present, can include one or more of PEG-diacylglycerol (DAG) (such as 1-(monomethoxy-polyethyleneglycol)-2,3-dimyristoylglycerol (PEG-DMG)), PEG-dialkyloxypropyl (DAA), PEG-phospholipid, PEG-ceramide (Cer), a pegylated phosphatidylethanolamine (PEG-PE), PEG succinate diacylglycerol (PEGS-DAG) (such as 4-0-(2′,3′-di(tetradecanoyloxy)propyl-1-0-(w-methoxy(polyethoxy)ethyl) butanedioate (PEG-S-DMG)), PEG dialkoxypropylcarbam, N-(carbonyl-methoxypoly ethylene glycol 2000)-1,2-distearoyl-sn-glycero-3-phosphoethanolamine sodium salt, and those described in Table 2 of WO2019051289 (incorporated by reference), and combinations of the foregoing.

In some embodiments, sterols that can be incorporated into lipid nanoparticles include one or more of cholesterol or cholesterol derivatives, such as those in WO2009/127060 or US2010/0130588, which are incorporated by reference. Additional exemplary sterols include phytosterols, including those described in Eygeris et al (2020), dx.doi.org/10.1021/acs.nanolett.0c01386, incorporated herein by reference.

In some embodiments, the lipid particle comprises an ionizable lipid, a non-cationic lipid, a conjugated lipid that inhibits aggregation of particles, and a sterol. The amounts of these components can be varied independently and to achieve desired properties. For example, in some embodiments, the lipid nanoparticle comprises an ionizable lipid is in an amount from about 20 mol % to about 90 mol % of the total lipids (in other embodiments it may be 20-70% (mol), 30-60% (mol) or 40-50% (mol); about 50 mol % to about 90 mol % of the total lipid present in the lipid nanoparticle), a non-cationic lipid in an amount from about 5 mol % to about 30 mol % of the total lipids, a conjugated lipid in an amount from about 0.5 mol % to about 20 mol % of the total lipids, and a sterol in an amount from about 20 mol % to about 50 mol % of the total lipids. The ratio of total lipid to nucleic acid (e.g., encoding the gene modifying polypeptide or template nucleic acid) can be varied as desired. For example, the total lipid to nucleic acid (mass or weight) ratio can be from about 10:1 to about 30:1.

In some embodiments, an ionizable lipid may be a cationic lipid, an ionizable cationic lipid, e.g., a cationic lipid that can exist in a positively charged or neutral form depending on pH, or an amine-containing lipid that can be readily protonated. In some embodiments, the cationic lipid is a lipid capable of being positively charged, e.g., under physiological conditions. Exemplary cationic lipids include one or more amine group(s) which bear the positive charge. In some embodiments, the lipid particle comprises a cationic lipid in formulation with one or more of neutral lipids, ionizable amine-containing lipids, biodegradable alkyn lipids, steroids, phospholipids including polyunsaturated lipids, structural lipids (e.g., sterols), PEG, cholesterol and polymer conjugated lipids. In some embodiments, the cationic lipid may be an ionizable cationic lipid. An exemplary cationic lipid as disclosed herein may have an effective pKa over 6.0. In embodiments, a lipid nanoparticle may comprise a second cationic lipid having a different effective pKa (e.g., greater than the first effective pKa), than the first cationic lipid. A lipid nanoparticle may comprise between 40 and 60 mol percent of a cationic lipid, a neutral lipid, a steroid, a polymer conjugated lipid, and a therapeutic agent, e.g., a nucleic acid (e.g., RNA) described herein (e.g., a template nucleic acid or a nucleic acid encoding a gene modifying polypeptide), encapsulated within or associated with the lipid nanoparticle. In some embodiments, the nucleic acid is co-formulated with the cationic lipid. The nucleic acid may be adsorbed to the surface of an LNP, e.g., an LNP comprising a cationic lipid. In some embodiments, the nucleic acid may be encapsulated in an LNP, e.g., an LNP comprising a cationic lipid. In some embodiments, the lipid nanoparticle may comprise a targeting moiety, e.g., coated with a targeting agent. In embodiments, the LNP formulation is biodegradable. In some embodiments, a lipid nanoparticle comprising one or more lipid described herein, e.g., Formula (i), (ii), (ii), (vii) and/or (ix) encapsulates at least 1%, at least 5%, at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 92%, at least 95%, at least 97%, at least 98% or 100% of an RNA molecule, e.g., template RNA and/or a mRNA encoding the gene modifying polypeptide.

In some embodiments, the lipid to nucleic acid ratio (mass/mass ratio; w/w ratio) can be in the range of from about 1:1 to about 25:1, from about 10:1 to about 14:1, from about 3:1 to about 15:1, from about 4:1 to about 10:1, from about 5:1 to about 9:1, or about 6:1 to about 9:1. The amounts of lipids and nucleic acid can be adjusted to provide a desired N/P ratio, for example, N/P ratio of 3, 4, 5, 6, 7, 8, 9, 10 or higher. Generally, the lipid nanoparticle formulation's overall lipid content can range from about 5 mg/ml to about 30 mg/mL.

Exemplary ionizable lipids that can be used in lipid nanoparticle formulations include, without limitation, those listed in Table 1 of WO2019051289, incorporated herein by reference. Additional exemplary lipids include, without limitation, one or more of the following formulae: X of US2016/0311759; I of US20150376115 or in US2016/0376224; I, II or III of US20160151284; I, IA, II, or IIA of US20170210967; I-c of US20150140070; A of US2013/0178541; I of US2013/0303587 or US2013/0123338; I of US2015/0141678; II, III, IV, or V of US2015/0239926; I of US2017/0119904; I or II of WO2017/117528; A of US2012/0149894; A of US2015/0057373; A of WO2013/116126; A of US2013/0090372; A of US2013/0274523; A of US2013/0274504; A of US2013/0053572; A of WO2013/016058; A of WO2012/162210; I of US2008/042973; I, II, III, or IV of US2012/01287670; I or II of US2014/0200257; 1, 11, or III of US2015/0203446; I or III of US2015/0005363; I, IA, IB, IC, ID, II, IIA, IIB, IIC, IID, or III-XXIV of US2014/0308304; of US2013/0338210; I, II, III, or IV of WO2009/132131; A of US2012/01011478; I or XXXV of US2012/0027796; XIV or XVII of US2012/0058144; of US2013/0323269; I of US2011/0117125; I, II, or III of US2011/0256175; I, II, III, IV, V, VI, VII, VIII, IX, X, XI, XII of US2012/0202871; I, II, III, IV, V, VI, VII, VIII, X, XII, XIII, XIV, XV, or XVI of US2011/0076335; I or II of US2006/008378; I of US2013/0123338; I or X-A-Y-Z of US2015/0064242; XVI, XVII, or XVIII of US2013/0022649; I, II, or III of US2013/0116307; I, II, or III of US2013/0116307; I or II of US2010/0062967; I-X of US2013/0189351; I of US2014/0039032; V of US2018/0028664; I of US2016/0317458; I of US2013/0195920; 5, 6, or 10 of U.S. Pat. No. 10,221,127; III-3 of WO2018/081480; I-5 or I-8 of WO2020/081938; 18 or 25 of U.S. Pat. No. 9,867,888; A of US2019/0136231; II of WO2020/219876; 1 of US2012/0027803; OF-02 of US2019/0240349; 23 of U.S. Pat. No. 10,086,013; cKK-E12/A6 of Miao et al (2020); C12-200 of WO2010/053572; 7C1 of Dahlman et al (2017); 304-013 or 503-013 of Whitehead et al; TS-P4C2 of U.S. Pat. No. 9,708,628; I of WO2020/106946; I of WO2020/106946.

In some embodiments, the ionizable lipid is MC3 (6Z,9Z,28Z,31Z)-heptatriaconta-6,9,28,31-tetraen-19-yl-4-(dimethylamino) butanoate (DLin-MC3-DMA or MC3), e.g., as described in Example 9 of WO2019051289A9 (incorporated by reference herein in its entirety). In some embodiments, the ionizable lipid is the lipid ATX-002, e.g., as described in Example 10 of WO2019051289A9 (incorporated by reference herein in its entirety). In some embodiments, the ionizable lipid is (13Z,16Z)-A,A-dimethyl-3-nonyldocosa-13,16-dien-1-amine (Compound 32), e.g., as described in Example 11 of WO2019051289A9 (incorporated by reference herein in its entirety). In some embodiments, the ionizable lipid is Compound 6 or Compound 22, e.g., as described in Example 12 of WO2019051289A9 (incorporated by reference herein in its entirety). In some embodiments, the ionizable lipid is heptadecan-9-yl 8-((2-hydroxyethyl)(6-oxo-6-(undecyloxy)hexyl)amino)octanoate (SM-102); e.g., as described in Example 1 of U.S. Pat. No. 9,867,888 (incorporated by reference herein in its entirety). In some embodiments, the ionizable lipid is 9Z,12Z)-3-((4,4-bis(octyloxy)butanoyl)oxy)-2-((((3-(diethylamino)propoxy)carbonyl)oxy)methyl)propyl octadeca-9,12-dienoate (LP01) e.g., as synthesized in Example 13 of WO2015/095340 (incorporated by reference herein in its entirety). In some embodiments, the ionizable lipid is Di((Z)-non-2-en-1-yl) 9-((4-dimethylamino)butanoyl)oxy)heptadecanedioate (L319), e.g. as synthesized in Example 7, 8, or 9 of US2012/0027803 (incorporated by reference herein in its entirety). In some embodiments, the ionizable lipid is 1,1′-((2-(4-(2-((2-(Bis(2-hydroxydodecyl)amino)ethyl)(2-hydroxydodecyl)amino)ethyl)piperazin-1-yl)ethyl)azanediyl)bis(dodecan-2-ol) (C12-200), e.g., as synthesized in Examples 14 and 16 of WO2010/053572 (incorporated by reference herein in its entirety). In some embodiments, the ionizable lipid is; Imidazole cholesterol ester (ICE) lipid (3S, 10R, 13R, 17R)-10,13-dimethyl-17-((R)-6-methylheptan-2-yl)-2, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17-tetradecahydro-1H-cyclopenta[a]phenanthren-3-yl 3-(1H-imidazol-4-yl)propanoate, e.g., Structure (I) from WO2020/106946 (incorporated by reference herein in its entirety).

Some non-limiting examples of lipid compounds that may be used (e.g., in combination with other lipid components) to form lipid nanoparticles for the delivery of compositions described herein, e.g., nucleic acid (e.g., RNA) described herein (e.g., a template nucleic acid or a nucleic acid encoding a gene modifying polypeptide) includes,

In some embodiments an LNP comprising Formula (i) is used to deliver a gene modifying composition described herein to the liver and/or hepatocyte cells.

In some embodiments an LNP comprising Formula (ii) is used to deliver a gene modifying composition described herein to the liver and/or hepatocyte cells.

In some embodiments an LNP comprising Formula (iii) is used to deliver a gene modifying composition described herein to the liver and/or hepatocyte cells.

In some embodiments an LNP comprising Formula (v) is used to deliver a gene modifying composition described herein to the liver and/or hepatocyte cells.

In some embodiments an LNP comprising Formula (vi) is used to deliver a gene modifying composition described herein to the liver and/or hepatocyte cells.

In some embodiments an LNP comprising Formula (viii) is used to deliver a gene modifying composition described herein to the liver and/or hepatocyte cells.

In some embodiments an LNP comprising Formula (ix) is used to deliver a gene modifying composition described herein to the liver and/or hepatocyte cells.

-   -   wherein     -   X¹ is O, NR¹, or a direct bond, X² is C2-5 alkylene, X³ is C(═O)         or a direct bond, R¹ is H or Me, R³ is Ci-3 alkyl, R² is Ci-3         alkyl, or R² taken together with the nitrogen atom to which it         is attached and 1-3 carbon atoms of X² form a 4-, 5-, or         6-membered ring, or X¹ is NR¹, R¹ and R² taken together with the         nitrogen atoms to which they are attached form a 5- or         6-membered ring, or R² taken together with R³ and the nitrogen         atom to which they are attached form a 5-, 6-, or 7-membered         ring, Y¹ is C2-12 alkylene, Y² is selected from

-   -   n is 0 to 3, R⁴ is Ci-15 alkyl, Z¹ is Ci-6 alkylene or a direct         bond,     -   Z² is

-   -   (in either orientation) or absent, provided that if Z¹ is a         direct bond, Z² is absent;     -   R⁵ is C5-9 alkyl or C6-10 alkoxy, R⁶ is C5-9 alkyl or C6-10         alkoxy, W is methylene or a direct bond, and R⁷ is H or Me, or a         salt thereof, provided that if R³ and R² are C2 alkyls, X¹ is O,         X² is linear C3 alkylene, X³ is C(═O), Y¹ is linear Ce alkylene         (Y²)n-R⁴ is

-   -   R⁴ is linear C5 alkyl, Z¹ is C2 alkylene, Z² is absent, W is         methylene, and R⁷ is H, then R⁵ and R⁶ are not Cx alkoxy.

In some embodiments an LNP comprising Formula (xii) is used to deliver a gene modifying composition described herein to the liver and/or hepatocyte cells.

In some embodiments an LNP comprising Formula (xi) is used to deliver a gene modifying composition described herein to the liver and/or hepatocyte cells.

where

In some embodiments an LNP comprises a compound of Formula (xiii) and a compound of Formula (xiv).

In some embodiments an LNP comprising Formula (xv) is used to deliver a gene modifying composition described herein to the liver and/or hepatocyte cells.

In some embodiments an LNP comprising a formulation of Formula (xvi) is used to deliver a gene modifying composition described herein to the lung endothelial cells.

In some embodiments, a lipid compound used to form lipid nanoparticles for the delivery of compositions described herein, e.g., nucleic acid (e.g., RNA) described herein (e.g., a template nucleic acid or a nucleic acid encoding a gene modifying polypeptide) is made by one of the following reactions:

Exemplary non-cationic lipids include, but are not limited to, distearoyl-sn-glycero-phosphoethanolamine, distearoylphosphatidylcholine (DSPC), dioleoylphosphatidylcholine (DOPC), dipalmitoylphosphatidylcholine (DPPC), dioleoylphosphatidylglycerol (DOPG), dipalmitoylphosphatidylglycerol (DPPG), dioleoyl-phosphatidylethanolamine (DOPE), 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE), palmitoyloleoylphosphatidylcholine (POPC), palmitoyloleoylphosphatidylethanolamine (POPE), dioleoyl-phosphatidylethanolamine 4-(N-maleimidomethyl)-cyclohexane-1-carboxylate (DOPE-mal), dipalmitoyl phosphatidyl ethanolamine (DPPE), dimyristoylphosphoethanolamine (DMPE), distearoyl-phosphatidyl-ethanolamine (DSPE), monomethyl-phosphatidylethanolamine (such as 16-O-monomethyl PE), dimethyl-phosphatidylethanolamine (such as 16-O-dimethyl PE), 18-1-trans PE, 1-stearoyl-2-oleoyl-phosphatidyethanolamine (SOPE), hydrogenated soy phosphatidylcholine (HSPC), egg phosphatidylcholine (EPC), dioleoylphosphatidylserine (DOPS), sphingomyelin (SM), dimyristoyl phosphatidylcholine (DMPC), dimyristoyl phosphatidylglycerol (DMPG), distearoylphosphatidylglycerol (DSPG), dierucoylphosphatidylcholine (DEPC), palmitoyloleyolphosphatidylglycerol (POPG), dielaidoyl-phosphatidylethanolamine (DEPE), lecithin, phosphatidylethanolamine, lysolecithin, lysophosphatidylethanolamine, phosphatidylserine, phosphatidylinositol, sphingomyelin, egg sphingomyelin (ESM), cephalin, cardiolipin, phosphatidicacid, cerebrosides, dicetylphosphate, lysophosphatidylcholine, dilinoleoylphosphatidylcholine, or mixtures thereof. It is understood that other diacylphosphatidylcholine and diacylphosphatidylethanolamine phospholipids can also be used. The acyl groups in these lipids are preferably acyl groups derived from fatty acids having C10-C24 carbon chains, e.g., lauroyl, myristoyl, palmitoyl, stearoyl, or oleoyl. Additional exemplary lipids, in certain embodiments, include, without limitation, those described in Kim et al. (2020) dx.doi.org/10.1021/acs.nanolett.0c01386, incorporated herein by reference. Such lipids include, in some embodiments, plant lipids found to improve liver transfection with mRNA (e.g., DGTS). In some embodiments, the non-cationic lipid may have the following structure,

Other examples of non-cationic lipids suitable for use in the lipid nanoparticles include, without limitation, nonphosphorous lipids such as, e.g., stearylamine, dodecylamine, hexadecylamine, acetyl palmitate, glycerol ricinoleate, hexadecyl stearate, isopropyl myristate, amphoteric acrylic polymers, triethanolamine-lauryl sulfate, alkyl-aryl sulfate polyethyoxylated fatty acid amides, dioctadecyl dimethyl ammonium bromide, ceramide, sphingomyelin, and the like. Other non-cationic lipids are described in WO2017/099823 or US patent publication US2018/0028664, the contents of which is incorporated herein by reference in their entirety.

In some embodiments, the non-cationic lipid is oleic acid or a compound of Formula I, II, or IV of US2018/0028664, incorporated herein by reference in its entirety. The non-cationic lipid can comprise, for example, 0-30% (mol) of the total lipid present in the lipid nanoparticle. In some embodiments, the non-cationic lipid content is 5-20% (mol) or 10-15% (mol) of the total lipid present in the lipid nanoparticle. In embodiments, the molar ratio of ionizable lipid to the neutral lipid ranges from about 2:1 to about 8:1 (e.g., about 2:1, 3:1, 4:1, 5:1, 6:1, 7:1, or 8:1).

In some embodiments, the lipid nanoparticles do not comprise any phospholipids.

In some embodiments, the lipid nanoparticle can further comprise a component, such as a sterol, to provide membrane integrity. One exemplary sterol that can be used in the lipid nanoparticle is cholesterol and derivatives thereof. Non-limiting examples of cholesterol derivatives include polar analogues such as 5a-cholestanol, 53-coprostanol, cholesteryl-(2′-hydroxy)-ethyl ether, cholesteryl-(4′-hydroxy)-butyl ether, and 6-ketocholestanol; non-polar analogues such as 5a-cholestane, cholestenone, 5a-cholestanone, 5p-cholestanone, and cholesteryl decanoate; and mixtures thereof. In some embodiments, the cholesterol derivative is a polar analogue, e.g., cholesteryl-(4′-hydroxy)-butyl ether. Exemplary cholesterol derivatives are described in PCT publication WO2009/127060 and US patent publication US2010/0130588, each of which is incorporated herein by reference in its entirety.

In some embodiments, the component providing membrane integrity, such as a sterol, can comprise 0-50% (mol) (e.g., 0-10%, 10-20%, 20-30%, 30-40%, or 40-50%) of the total lipid present in the lipid nanoparticle. In some embodiments, such a component is 20-50% (mol) 30-40% (mol) of the total lipid content of the lipid nanoparticle.

In some embodiments, the lipid nanoparticle can comprise a polyethylene glycol (PEG) or a conjugated lipid molecule. Generally, these are used to inhibit aggregation of lipid nanoparticles and/or provide steric stabilization. Exemplary conjugated lipids include, but are not limited to, PEG-lipid conjugates, polyoxazoline (POZ)-lipid conjugates, polyamide-lipid conjugates (such as ATTA-lipid conjugates), cationic-polymer lipid (CPL) conjugates, and mixtures thereof. In some embodiments, the conjugated lipid molecule is a PEG-lipid conjugate, for example, a (methoxy polyethylene glycol)-conjugated lipid.

Exemplary PEG-lipid conjugates include, but are not limited to, PEG-diacylglycerol (DAG) (such as 1-(monomethoxy-polyethyleneglycol)-2,3-dimyristoylglycerol (PEG-DMG)), PEG-dialkyloxypropyl (DAA), PEG-phospholipid, PEG-ceramide (Cer), a pegylated phosphatidylethanolamine (PEG-PE), 1,2-dimyristoyl-sn-glycerol, methoxypoly ethylene glycol (DMG-PEG-2K), PEG succinate diacylglycerol (PEGS-DAG) (such as 4-0-(2′,3′-di(tetradecanoyloxy)propyl-1-0-(w-methoxy(polyethoxy)ethyl) butanedioate (PEG-S-DMG)), PEG dialkoxypropylcarbam, N-(carbonyl-methoxypolyethylene glycol 2000)-1,2-distearoyl-sn-glycero-3-phosphoethanolamine sodium salt, or a mixture thereof. Additional exemplary PEG-lipid conjugates are described, for example, in U.S. Pat. Nos. 5,885,613, 6,287,591, US2003/0077829, US2003/0077829, US2005/0175682, US2008/0020058, US2011/0117125, US2010/0130588, US2016/0376224, US2017/0119904, and US/099823, the contents of all of which are incorporated herein by reference in their entirety. In some embodiments, a PEG-lipid is a compound of Formula III, III-a-I, III-a-2, III-b-1, III-b-2, or V of US2018/0028664, the content of which is incorporated herein by reference in its entirety. In some embodiments, a PEG-lipid is of Formula II of US20150376115 or US2016/0376224, the content of both of which is incorporated herein by reference in its entirety. In some embodiments, the PEG-DAA conjugate can be, for example, PEG-dilauryloxypropyl, PEG-dimyristyloxypropyl, PEG-dipalmityloxypropyl, or PEG-distearyloxypropyl. The PEG-lipid can be one or more of PEG-DMG, PEG-dilaurylglycerol, PEG-dipalmitoylglycerol, PEG-distearoylglycerol, PEG-dilaurylglycamide, PEG-dimyristylglycamide, PEG-dipalmitoylglycamide, PEG-disterylglycamide, PEG-cholesterol (1-[8′-(Cholest-5-en-3[beta]-oxy)carboxamido-3′,6′-dioxaoctanyl]carbamoyl-[omega]-methyl-poly(ethylene glycol), PEG-DMB (3,4-Ditetradecoxylbenzyl-[omega]-methyl-poly(ethylene glycol) ether), and 1,2-dimyristoyl-sn-glycero-3-phosphoethanolamine-N-[methoxy(polyethylene glycol)-2000]. In some embodiments, the PEG-lipid comprises PEG-DMG, 1,2-dimyristoyl-sn-glycero-3-phosphoethanolamine-N-[methoxy(polyethylene glycol)-2000]. In some embodiments, the PEG-lipid comprises a structure selected from:

In some embodiments, lipids conjugated with a molecule other than a PEG can also be used in place of PEG-lipid. For example, polyoxazoline (POZ)-lipid conjugates, polyamide-lipid conjugates (such as ATTA-lipid conjugates), and cationic-polymer lipid (GPL) conjugates can be used in place of or in addition to the PEG-lipid.

Exemplary conjugated lipids, i.e., PEG-lipids, (POZ)-lipid conjugates, ATTA-lipid conjugates and cationic polymer-lipids are described in the PCT and LIS patent applications listed in Table 2 of WO2019051289A9 and in WO2020106946A1, the contents of all of which are incorporated herein by reference in their entirety.

In some embodiments an LNP comprises a compound of Formula (xix), a compound of Formula (xxi) and a compound of Formula (xxv). In some embodiments an LNP comprising a formulation of Formula (xix), Formula (xxi) and Formula (xxv) is used to deliver a gene modifying composition described herein to the lung or pulmonary cells.

In some embodiments, a lipid nanoparticle may comprise one or more cationic lipids selected from Formula (i), Formula (ii), Formula (iii), Formula (vii), and Formula (ix). In some embodiments, the LNP may further comprise one or more neutral lipid, e.g., DSPC, DPPC, DMPC, DOPC, POPC, DOPE, SM, a steroid, e.g., cholesterol, and/or one or more polymer conjugated lipid, e.g., a pegylated lipid, e.g., PEG-DAG, PEG-PE, PEG-S-DAG, PEG-cer or a PEG dialkyoxypropylcarbamate.

In some embodiments, the PEG or the conjugated lipid can comprise 0-20% (mol) of the total lipid present in the lipid nanoparticle. In some embodiments, PEG or the conjugated lipid content is 0.5-10% or 2-5% (mol) of the total lipid present in the lipid nanoparticle. Molar ratios of the ionizable lipid, non-cationic-lipid, sterol, and PEG/conjugated lipid can be varied as needed. For example, the lipid particle can comprise 30-70% ionizable lipid by mole or by total weight of the composition, 0-60% cholesterol by mole or by total weight of the composition, 0-30% non-cationic-lipid by mole or by total weight of the composition and 1-10% conjugated lipid by mole or by total weight of the composition. Preferably, the composition comprises 30-40% ionizable lipid by mole or by total weight of the composition, 40-50% cholesterol by mole or by total weight of the composition, and 10-20% non-cationic-lipid by mole or by total weight of the composition. In some other embodiments, the composition is 50-75% ionizable lipid by mole or by total weight of the composition, 20-40% cholesterol by mole or by total weight of the composition, and 5 to 10% non-cationic-lipid, by mole or by total weight of the composition and 1-10% conjugated lipid by mole or by total weight of the composition. The composition may contain 60-70% ionizable lipid by mole or by total weight of the composition, 25-35% cholesterol by mole or by total weight of the composition, and 5-10% non-cationic-lipid by mole or by total weight of the composition. The composition may also contain up to 90% ionizable lipid by mole or by total weight of the composition and 2 to 15% non-cationic lipid by mole or by total weight of the composition. The formulation may also be a lipid nanoparticle formulation, for example comprising 8-30% ionizable lipid by mole or by total weight of the composition, 5-30% non-cationic lipid by mole or by total weight of the composition, and 0-20% cholesterol by mole or by total weight of the composition; 4-25% ionizable lipid by mole or by total weight of the composition, 4-25% non-cationic lipid by mole or by total weight of the composition, 2 to 25% cholesterol by mole or by total weight of the composition, 10 to 35% conjugate lipid by mole or by total weight of the composition, and 5% cholesterol by mole or by total weight of the composition; or 2-30% ionizable lipid by mole or by total weight of the composition, 2-30% non-cationic lipid by mole or by total weight of the composition, 1 to 15% cholesterol by mole or by total weight of the composition, 2 to 35% conjugate lipid by mole or by total weight of the composition, and 1-20% cholesterol by mole or by total weight of the composition; or even up to 90% ionizable lipid by mole or by total weight of the composition and 2-10% non-cationic lipids by mole or by total weight of the composition, or even 100% cationic lipid by mole or by total weight of the composition. In some embodiments, the lipid particle formulation comprises ionizable lipid, phospholipid, cholesterol and a PEG-ylated lipid in a molar ratio of 50:10:38.5:1.5. In some other embodiments, the lipid particle formulation comprises ionizable lipid, cholesterol and a PEG-ylated lipid in a molar ratio of 60:38.5:1.5.

In some embodiments, the lipid particle comprises ionizable lipid, non-cationic lipid (e.g. phospholipid), a sterol (e.g., cholesterol) and a PEG-ylated lipid, where the molar ratio of lipids ranges from 20 to 70 mole percent for the ionizable lipid, with a target of 40-60, the mole percent of non-cationic lipid ranges from 0 to 30, with a target of 0 to 15, the mole percent of sterol ranges from 20 to 70, with a target of 30 to 50, and the mole percent of PEG-ylated lipid ranges from 1 to 6, with a target of 2 to 5.

In some embodiments, the lipid particle comprises ionizable lipid/non-cationic-lipid/sterol/conjugated lipid at a molar ratio of 50:10:38.5:1.5.

In an aspect, the disclosure provides a lipid nanoparticle formulation comprising phospholipids, lecithin, phosphatidylcholine and phosphatidylethanolamine.

In some embodiments, one or more additional compounds can also be included. Those compounds can be administered separately or the additional compounds can be included in the lipid nanoparticles of the invention. In other words, the lipid nanoparticles can contain other compounds in addition to the nucleic acid or at least a second nucleic acid, different than the first. Without limitations, other additional compounds can be selected from the group consisting of small or large organic or inorganic molecules, monosaccharides, disaccharides, trisaccharides, oligosaccharides, polysaccharides, peptides, proteins, peptide analogs and derivatives thereof, peptidomimetics, nucleic acids, nucleic acid analogs and derivatives, an extract made from biological materials, or any combinations thereof.

In some embodiments, a lipid nanoparticle (or a formulation comprising lipid nanoparticles) lacks reactive impurities (e.g., aldehydes or ketones), or comprises less than a preselected level of reactive impurities (e.g., aldehydes or ketones). While not wishing to be bound by theory, in some embodiments, a lipid reagent is used to make a lipid nanoparticle formulation, and the lipid reagent may comprise a contaminating reactive impurity (e.g., an aldehyde or ketone). A lipid regent may be selected for manufacturing based on having less than a preselected level of reactive impurities (e.g., aldehydes or ketones). Without wishing to be bound by theory, in some embodiments, aldehydes can cause modification and damage of RNA, e.g., cross-linking between bases and/or covalently conjugating lipid to RNA (e.g., forming lipid-RNA adducts). This may, in some instances, lead to failure of a reverse transcriptase reaction and/or incorporation of inappropriate bases, e.g., at the site(s) of lesion(s), e.g., a mutation in a newly synthesized target DNA.

In some embodiments, a lipid nanoparticle formulation is produced using a lipid reagent comprising less than 5%, 4%, 3%, 2%, 1%, 0.9%, 0.8%, 0.7%, 0.6%, 0.5%, 0.4%, 0.3%, 0.2%, or 0.1% total reactive impurity (e.g., aldehyde) content. In some embodiments, a lipid nanoparticle formulation is produced using a lipid reagent comprising less than 5%, 4%, 3%, 2%, 1%, 0.9%, 0.8%, 0.7%, 0.6%, 0.5%, 0.4%, 0.3%, 0.2%, or 0.1% of any single reactive impurity (e.g., aldehyde) species. In some embodiments, a lipid nanoparticle formulation is produced using a lipid reagent comprising: (i) less than 5%, 4%, 3%, 2%, 1%, 0.9%, 0.8%, 0.7%, 0.6%, 0.5%, 0.4%, 0.3%, 0.2%, or 0.1% total reactive impurity (e.g., aldehyde) content; and (ii) less than 5%, 4%, 3%, 2%, 1%, 0.9%, 0.8%, 0.7%, 0.6%, 0.5%, 0.4%, 0.3%, 0.2%, or 0.1% of any single reactive impurity (e.g., aldehyde) species. In some embodiments, the lipid nanoparticle formulation is produced using a plurality of lipid reagents, and each lipid reagent of the plurality independently meets one or more criterion described in this paragraph. In some embodiments, each lipid reagent of the plurality meets the same criterion, e.g., a criterion of this paragraph.

In some embodiments, the lipid nanoparticle formulation comprises less than 5%, 4%, 3%, 2%, 1%, 0.9%, 0.8%, 0.7%, 0.6%, 0.5%, 0.4%, 0.3%, 0.2%, or 0.1% total reactive impurity (e.g., aldehyde) content. In some embodiments, the lipid nanoparticle formulation comprises less than 5%, 4%, 3%, 2%, 1%, 0.9%, 0.8%, 0.7%, 0.6%, 0.5%, 0.4%, 0.3%, 0.2%, or 0.1% of any single reactive impurity (e.g., aldehyde) species. In some embodiments, the lipid nanoparticle formulation comprises: (i) less than 5%, 4%, 3%, 2%, 1%, 0.9%, 0.8%, 0.7%, 0.6%, 0.5%, 0.4%, 0.3%, 0.2%, or 0.1% total reactive impurity (e.g., aldehyde) content; and (ii) less than 5%, 4%, 3%, 2%, 1%, 0.9%, 0.8%, 0.7%, 0.6%, 0.5%, 0.4%, 0.3%, 0.2%, or 0.1% of any single reactive impurity (e.g., aldehyde) species.

In some embodiments, one or more, or optionally all, of the lipid reagents used for a lipid nanoparticle as described herein or a formulation thereof comprise less than 5%, 4%, 3%, 2%, 1%, 0.9%, 0.8%, 0.7%, 0.6%, 0.5%, 0.4%, 0.3%, 0.2%, or 0.1% total reactive impurity (e.g., aldehyde) content. In some embodiments, one or more, or optionally all, of the lipid reagents used for a lipid nanoparticle as described herein or a formulation thereof comprise less than 5%, 4%, 3%, 2%, 1%, 0.9%, 0.8%, 0.7%, 0.6%, 0.5%, 0.4%, 0.3%, 0.2%, or 0.1% of any single reactive impurity (e.g., aldehyde) species. In some embodiments, one or more, or optionally all, of the lipid reagents used for a lipid nanoparticle as described herein or a formulation thereof comprise: (i) less than 5%, 4%, 3%, 2%, 1%, 0.9%, 0.8%, 0.7%, 0.6%, 0.5%, 0.4%, 0.3%, 0.2%, or 0.1% total reactive impurity (e.g., aldehyde) content; and (ii) less than 5%, 4%, 3%, 2%, 1%, 0.9%, 0.8%, 0.7%, 0.6%, 0.5%, 0.4%, 0.3%, 0.2%, or 0.1% of any single reactive impurity (e.g., aldehyde) species.

In some embodiments, total aldehyde content and/or quantity of any single reactive impurity (e.g., aldehyde) species is determined by liquid chromatography (LC), e.g., coupled with tandem mass spectrometry (MS/MS), e.g., according to the method described in Example 40 of PCT/US21/20948. In some embodiments, reactive impurity (e.g., aldehyde) content and/or quantity of reactive impurity (e.g., aldehyde) species is determined by detecting one or more chemical modifications of a nucleic acid molecule (e.g., an RNA molecule, e.g., as described herein) associated with the presence of reactive impurities (e.g., aldehydes), e.g., in the lipid reagents. In some embodiments, reactive impurity (e.g., aldehyde) content and/or quantity of reactive impurity (e.g., aldehyde) species is determined by detecting one or more chemical modifications of a nucleotide or nucleoside (e.g., a ribonucleotide or ribonucleoside, e.g., comprised in or isolated from a template nucleic acid, e.g., as described herein) associated with the presence of reactive impurities (e.g., aldehydes), e.g., in the lipid reagents, e.g., according to the method described in Example 41 of PCT/US21/20948. In embodiments, chemical modifications of a nucleic acid molecule, nucleotide, or nucleoside are detected by determining the presence of one or more modified nucleotides or nucleosides, e.g., using LC-MS/MS analysis, e.g., according to the method described in Example 41 of PCT/US21/20948.

In some embodiments, a nucleic acid (e.g., RNA) described herein (e.g., a template nucleic acid or a nucleic acid encoding a gene modifying polypeptide) does not comprise an aldehyde modification, or comprises less than a preselected amount of aldehyde modifications. In some embodiments, on average, a nucleic acid has less than 50, 20, 10, 5, 2, or 1 aldehyde modifications per 1000 nucleotides, e.g., wherein a single cross-linking of two nucleotides is a single aldehyde modification. In some embodiments, the aldehyde modification is an RNA adduct (e.g., a lipid-RNA adduct). In some embodiments, the aldehyde-modified nucleotide is cross-linking between bases. In some embodiments, a nucleic acid (e.g., RNA) described herein comprises less than 50, 20, 10, 5, 2, or 1 cross-links between nucleotide.

In some embodiments, LNPs are directed to specific tissues by the addition of targeting domains. For example, biological ligands may be displayed on the surface of LNPs to enhance interaction with cells displaying cognate receptors, thus driving association with and cargo delivery to tissues wherein cells express the receptor. In some embodiments, the biological ligand may be a ligand that drives delivery to the liver, e.g., LNPs that display GalNAc result in delivery of nucleic acid cargo to hepatocytes that display asialoglycoprotein receptor (ASGPR). The work of Akinc et al. Mol Ther 18(7):1357-1364 (2010) teaches the conjugation of a trivalent GalNAc ligand to a PEG-lipid (GalNAc-PEG-DSG) to yield LNPs dependent on ASGPR for observable LNP cargo effect (see, e.g., FIG. 6 therein). Other ligand-displaying LNP formulations, e.g., incorporating folate, transferrin, or antibodies, are discussed in WO2017223135, which is incorporated herein by reference in its entirety, in addition to the references used therein, namely Kolhatkar et al., Curr Drug Discov Technol. 2011 8:197-206; Musacchio and Torchilin, Front Biosci. 2011 16:1388-1412; Yu et al., Mol Membr Biol. 2010 27:286-298; Patil et al., Crit Rev Ther Drug Carrier Syst. 2008 25:1-61; Benoit et al., Biomacromolecules. 2011 12:2708-2714; Zhao et al., Expert Opin Drug Deliv. 2008 5:309-319; Akinc et al., Mol Ther. 2010 18:1357-1364; Srinivasan et al., Methods Mol Biol. 2012 820:105-116; Ben-Arie et al., Methods Mol Biol. 2012 757:497-507; Peer 2010 J Control Release. 20:63-68; Peer et al., Proc Natl Acad Sci USA. 2007 104:4095-4100; Kim et al., Methods Mol Biol. 2011 721:339-353; Subramanya et al., Mol Ther. 2010 18:2028-2037; Song et al., Nat Biotechnol. 2005 23:709-717; Peer et al., Science. 2008 319:627-630; and Peer and Lieberman, Gene Ther. 2011 18:1127-1133.

In some embodiments, LNPs are selected for tissue-specific activity by the addition of a Selective ORgan Targeting (SORT) molecule to a formulation comprising traditional components, such as ionizable cationic lipids, amphipathic phospholipids, cholesterol and poly(ethylene glycol) (PEG) lipids. The teachings of Cheng et al. Nat Nanotechnol 15(4):313-320 (2020) demonstrate that the addition of a supplemental “SORT” component precisely alters the in vivo RNA delivery profile and mediates tissue-specific (e.g., lungs, liver, spleen) gene delivery and editing as a function of the percentage and biophysical property of the SORT molecule.

In some embodiments, the LNPs comprise biodegradable, ionizable lipids. In some embodiments, the LNPs comprise (9Z,12Z)-3-((4,4-bis(octyloxy)butanoyl)oxy)-2-((((3-(diethylamino)propoxy)carbonyl)oxy)methyl)propyl octadeca-9,12-dienoate, also called 3-((4,4-bis(octyloxy)butanoyl)oxy)-2-((((3-(diethylamino)propoxy)carbonyl)oxy)methyl)propyl (9Z,12Z)-octadeca-9,12-dienoate) or another ionizable lipid. See, e.g, lipids of WO2019/067992, WO/2017/173054, WO2015/095340, and WO2014/136086, as well as references provided therein. In some embodiments, the term cationic and ionizable in the context of LNP lipids is interchangeable, e.g., wherein ionizable lipids are cationic depending on the pH.

In some embodiments, an LNP described herein comprises a lipid described in Table 19

TABLE 19 Exemplary lipids Molecular LIPID ID Chemical Name Weight Structure LIPIDV003 (9Z,12Z)-3-((4,4- bis(octyloxy)butanoyl) oxy)-2-((((3-(diethylamino)propoxy) carbonyl)oxy)methyl)propyl octadeca-9,12-dienoate 852.29

LIPIDV004 Heptadecan-9-yl 8-((2-hydroxyethyl)(8- (nonyloxy)-8-oxooctyl)amino)octanoate 710.18

LIPIDV005 919.56

In some embodiments, multiple components of a gene modifying system may be prepared as a single LNP formulation, e.g., an LNP formulation comprises mRNA encoding for the gene modifying polypeptide and an RNA template. Ratios of nucleic acid components may be varied in order to maximize the properties of a therapeutic. In some embodiments, the ratio of RNA template to mRNA encoding a gene modifying polypeptide is about 1:1 to 100:1, e.g., about 1:1 to 20:1, about 20:1 to 40:1, about 40:1 to 60:1, about 60:1 to 80:1, or about 80:1 to 100:1, by molar ratio. In other embodiments, a system of multiple nucleic acids may be prepared by separate formulations, e.g., one LNP formulation comprising a template RNA and a second LNP formulation comprising an mRNA encoding a gene modifying polypeptide. In some embodiments, the system may comprise more than two nucleic acid components formulated into LNPs. In some embodiments, the system may comprise a protein, e.g., a gene modifying polypeptide, and a template RNA formulated into at least one LNP formulation.

In some embodiments, the average LNP diameter of the LNP formulation may be between 10s of nm and 100s of nm, e.g., measured by dynamic light scattering (DLS). In some embodiments, the average LNP diameter of the LNP formulation may be from about 40 nm to about 150 nm, such as about 40 nm, 45 nm, 50 nm, 55 nm, 60 nm, 65 nm, 70 nm, 75 nm, 80 nm, 85 nm, 90 nm, 95 nm, 100 nm, 105 nm, 110 nm, 115 nm, 120 nm, 125 nm, 130 nm, 135 nm, 140 nm, 145 nm, or 150 nm. In some embodiments, the average LNP diameter of the LNP formulation may be from about 50 nm to about 100 nm, from about 50 nm to about 90 nm, from about 50 nm to about 80 nm, from about 50 nm to about 70 nm, from about 50 nm to about 60 nm, from about 60 nm to about 100 nm, from about 60 nm to about 90 nm, from about 60 nm to about 80 nm, from about 60 nm to about 70 nm, from about 70 nm to about 100 nm, from about 70 nm to about 90 nm, from about 70 nm to about 80 nm, from about 80 nm to about 100 nm, from about 80 nm to about 90 nm, or from about 90 nm to about 100 nm. In some embodiments, the average LNP diameter of the LNP formulation may be from about 70 nm to about 100 nm. In a particular embodiment, the average LNP diameter of the LNP formulation may be about 80 nm. In some embodiments, the average LNP diameter of the LNP formulation may be about 100 nm. In some embodiments, the average LNP diameter of the LNP formulation ranges from about 1 mm to about 500 mm, from about 5 mm to about 200 mm, from about 10 mm to about 100 mm, from about 20 mm to about 80 mm, from about 25 mm to about 60 mm, from about 30 mm to about 55 mm, from about 35 mm to about 50 mm, or from about 38 mm to about 42 mm.

An LNP may, in some instances, be relatively homogenous. A polydispersity index may be used to indicate the homogeneity of an LNP, e.g., the particle size distribution of the lipid nanoparticles. A small (e.g., less than 0.3) polydispersity index generally indicates a narrow particle size distribution. An LNP may have a polydispersity index from about 0 to about 0.25, such as 0.01, 0.02, 0.03, 0.04, 0.05, 0.06, 0.07, 0.08, 0.09, 0.10, 0.11, 0.12, 0.13, 0.14, 0.15, 0.16, 0.17, 0.18, 0.19, 0.20, 0.21, 0.22, 0.23, 0.24, or 0.25. In some embodiments, the polydispersity index of an LNP may be from about 0.10 to about 0.20.

The zeta potential of an LNP may be used to indicate the electrokinetic potential of the composition. In some embodiments, the zeta potential may describe the surface charge of an LNP. Lipid nanoparticles with relatively low charges, positive or negative, are generally desirable, as more highly charged species may interact undesirably with cells, tissues, and other elements in the body. In some embodiments, the zeta potential of an LNP may be from about −10 mV to about +20 mV, from about −10 mV to about +15 mV, from about −10 mV to about +10 mV, from about −10 mV to about +5 mV, from about −10 mV to about 0 mV, from about −10 mV to about −5 mV, from about −5 mV to about +20 mV, from about −5 mV to about +15 mV, from about −5 mV to about +10 mV, from about −5 mV to about +5 mV, from about −5 mV to about 0 mV, from about 0 mV to about +20 mV, from about 0 mV to about +15 mV, from about 0 mV to about +10 mV, from about 0 mV to about +5 mV, from about +5 mV to about +20 mV, from about +5 mV to about +15 mV, or from about +5 mV to about +10 mV.

The efficiency of encapsulation of a protein and/or nucleic acid, e.g., gene modifying polypeptide or mRNA encoding the polypeptide, describes the amount of protein and/or nucleic acid that is encapsulated or otherwise associated with an LNP after preparation, relative to the initial amount provided. The encapsulation efficiency is desirably high (e.g., close to 100%). The encapsulation efficiency may be measured, for example, by comparing the amount of protein or nucleic acid in a solution containing the lipid nanoparticle before and after breaking up the lipid nanoparticle with one or more organic solvents or detergents. An anion exchange resin may be used to measure the amount of free protein or nucleic acid (e.g., RNA) in a solution. Fluorescence may be used to measure the amount of free protein and/or nucleic acid (e.g., RNA) in a solution. For the lipid nanoparticles described herein, the encapsulation efficiency of a protein and/or nucleic acid may be at least 50%, for example 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%. In some embodiments, the encapsulation efficiency may be at least 80%. In some embodiments, the encapsulation efficiency may be at least 90%. In some embodiments, the encapsulation efficiency may be at least 95%.

An LNP may optionally comprise one or more coatings. In some embodiments, an LNP may be formulated in a capsule, film, or table having a coating. A capsule, film, or tablet including a composition described herein may have any useful size, tensile strength, hardness or density.

Additional exemplary lipids, formulations, methods, and characterization of LNPs are taught by WO2020061457, which is incorporated herein by reference in its entirety.

In some embodiments, in vitro or ex vivo cell lipofections are performed using Lipofectamine MessengerMax (Thermo Fisher) or TransIT-mRNA Transfection Reagent (Mirus Bio). In certain embodiments, LNPs are formulated using the GenVoy_ILM ionizable lipid mix (Precision NanoSystems). In certain embodiments, LNPs are formulated using 2,2-dilinoleyl-4-dimethylaminoethyl-[1,3]-dioxolane (DLin-KC2-DMA) or dilinoleylmethyl-4-dimethylaminobutyrate (DLin-MC3-DMA or MC3), the formulation and in vivo use of which are taught in Jayaraman et al. Angew Chem Int Ed Engl 51(34):8529-8533 (2012), incorporated herein by reference in its entirety.

LNP formulations optimized for the delivery of CRISPR-Cas systems, e.g., Cas9-gRNA RNP, gRNA, Cas9 mRNA, are described in WO2019067992 and WO2019067910, both incorporated by reference.

Additional specific LNP formulations useful for delivery of nucleic acids are described in U.S. Pat. Nos. 8,158,601 and 8,168,775, both incorporated by reference, which include formulations used in patisiran, sold under the name ONPATTRO.

Exemplary dosing of gene modifying LNP may include about 0.1, 0.25, 0.3, 0.5, 1, 2, 3, 4, 5, 6, 8, 10, or 100 mg/kg (RNA). Exemplary dosing of AAV comprising a nucleic acid encoding one or more components of the system may include an MOI of about 10¹¹, 10¹², 10¹³, and 10⁴ vg/kg.

Kits, Articles of Manufacture, and Pharmaceutical Compositions

In an aspect the disclosure provides a kit comprising a gene modifying polypeptide or a gene modifying system, e.g., as described herein. In some embodiments, the kit comprises a gene modifying polypeptide (or a nucleic acid encoding the polypeptide) and a template RNA (or DNA encoding the template RNA). In some embodiments, the kit further comprises a reagent for introducing the system into a cell, e.g., transfection reagent, LNP, and the like. In some embodiments, the kit is suitable for any of the methods described herein. In some embodiments, the kit comprises one or more elements, compositions (e.g., pharmaceutical compositions), gene modifying polypeptides, and/or gene modifying systems, or a functional fragment or component thereof, e.g., disposed in an article of manufacture. In some embodiments, the kit comprises instructions for use thereof.

In an aspect, the disclosure provides an article of manufacture, e.g., in which a kit as described herein, or a component thereof, is disposed.

In an aspect, the disclosure provides a pharmaceutical composition comprising a gene modifying polypeptide or a gene modifying system, e.g., as described herein. In some embodiments, the pharmaceutical composition further comprises a pharmaceutically acceptable carrier or excipient. In some embodiments, the pharmaceutical composition comprises a template RNA and/or an RNA encoding the polypeptide. In embodiments, the pharmaceutical composition has one or more (e.g., 1, 2, 3, or 4) of the following characteristics:

-   -   (a) less than 1% (e.g., less than 0.5%, 0.4%, 0.3%, 0.2%, or         0.1%) DNA template relative to the template RNA and/or the RNA         encoding the polypeptide, e.g., on a molar basis;     -   (b) less than 1% (e.g., less than 0.5%, 0.4%, 0.3%, 0.2%, or         0.1%) uncapped RNA relative to the template RNA and/or the RNA         encoding the polypeptide, e.g., on a molar basis;     -   (c) less than 1% (e.g., less than 0.5%, 0.4%, 0.3%, 0.2%, or         0.1%) partial length RNAs relative to the template RNA and/or         the RNA encoding the polypeptide, e.g., on a molar basis;     -   (d) substantially lacks unreacted cap dinucleotides.

Chemistry, Manufacturing, and Controls (CMC)

Purification of protein therapeutics is described, for example, in Franks, Protein Biotechnology: Isolation, Characterization, and Stabilization, Humana Press (2013); and in Cutler, Protein Purification Protocols (Methods in Molecular Biology), Humana Press (2010).

In some embodiments, a gene modifying system, polypeptide, and/or template nucleic acid (e.g., template RNA) conforms to certain quality standards. In some embodiments, a gene modifying system, polypeptide, and/or template nucleic acid (e.g., template RNA) produced by a method described herein conforms to certain quality standards. Accordingly, the disclosure is directed, in some aspects, to methods of manufacturing a gene modifying system, polypeptide, and/or template nucleic acid (e.g., template RNA) that conforms to certain quality standards, e.g., in which said quality standards are assayed. The disclosure is also directed, in some aspects, to methods of assaying said quality standards in a gene modifying system, polypeptide, and/or template nucleic acid (e.g., template RNA). In some embodiments, quality standards include, but are not limited to, one or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12) of the following:

-   -   (i) the length of the template RNA, e.g., whether the template         RNA has a length that is above a reference length or within a         reference length range, e.g., whether at least 80%, 85%, 90%,         95%, 96%, 97%, 98%, or 99% of the template RNA present is         greater than 100, 125, 150, 175, or 200 nucleotides long;     -   (ii) the presence, absence, and/or length of a polyA tail on the         template RNA, e.g., whether at least 80%, 85%, 90%, 95%, 96%,         97%, 98%, or 99% of the template RNA present contains a polyA         tail (e.g., a polyA tail that is at least 5, 10, 20, 30, 50, 70,         100 nucleotides in length (SEQ ID NO: 15471));     -   (iii) the presence, absence, and/or type of a 5′ cap on the         template RNA, e.g., whether at least 80%, 85%, 90%, 95%, 96%,         97%, 98%, or 99% of the template RNA present contains a 5′ cap,         e.g., whether that cap is a 7-methylguanosine cap, e.g., a         O-Me-m7G cap;     -   (iv) the presence, absence, and/or type of one or more modified         nucleotides (e.g., selected from pseudouridine, dihydrouridine,         inosine, 7-methylguanosine, 1-N-methylpseudouridine (1-Me-Ψ),         5-methoxyuridine (5-MO-U), 5-methylcytidine (5mC), or a locked         nucleotide) in the template RNA, e.g., whether at least 80%,         85%, 90%, 95%, 96%, 97%, 98%, or 99% of the template RNA present         contains one or more modified nucleotides;     -   (v) the stability of the template RNA (e.g., over time and/or         under a pre-selected condition), e.g., whether at least 80%,         85%, 90%, 95%, 96%, 97%, 98%, or 99% of the template RNA remains         intact (e.g., greater than 100, 125, 150, 175, or 200         nucleotides long) after a stability test;     -   (vi) the potency of the template RNA in a system for modifying         DNA, e.g., whether at least 1% of target sites are modified         after a system comprising the template RNA is assayed for         potency;     -   (vii) the length of the polypeptide, first polypeptide, or         second polypeptide, e.g., whether the polypeptide, first         polypeptide, or second polypeptide has a length that is above a         reference length or within a reference length range, e.g.,         whether at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% of         the polypeptide, first polypeptide, or second polypeptide         present is greater than 600, 650, 700, 750, 800, 850, 900, 950,         1000, 1050, 1100, 1150, 1200, 1250, 1300, 1350, 1400, 1450,         1500, 1600, 1700, 1800, 1900, or 2000 amino acids long (and         optionally, no larger than 2500, 2000, 1500, 1400, 1300, 1200,         1100, 1000, 900, 800, 700, or 600 amino acids long);     -   (viii) the presence, absence, and/or type of post-translational         modification on the polypeptide, first polypeptide, or second         polypeptide, e.g., whether at least 80, 85, 90, 95, 96, 97, 98,         or 99% of the polypeptide, first polypeptide, or second         polypeptide contains phosphorylation, methylation, acetylation,         myristoylation, palmitoylation, isoprenylation, glypiation, or         lipoylation, or any combination thereof;     -   (ix) the presence, absence, and/or type of one or more         artificial, synthetic, or non-canonical amino acids (e.g.,         selected from ornithine, β-alanine, GABA, δ-Aminolevulinic acid,         PABA, a D-amino acid (e.g., D-alanine or D-glutamate),         aminoisobutyric acid, dehydroalanine, cystathionine,         lanthionine, Djenkolic acid, Diaminopimelic acid, Homoalanine,         Norvaline, Norleucine, Homonorleucine, homoserine,         O-methyl-homoserine and O-ethyl-homoserine, ethionine,         selenocysteine, selenohomocysteine, selenomethionine,         selenomethionine, tellurocysteine, or telluromethionine) in the         polypeptide, first polypeptide, or second polypeptide, e.g.,         whether at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% of         the polypeptide, first polypeptide, or second polypeptide         present contains one or more artificial, synthetic, or         non-canonical amino acids;     -   (x) the stability of the polypeptide, first polypeptide, or         second polypeptide (e.g., over time and/or under a pre-selected         condition), e.g., whether at least 80%, 85%, 90%, 95%, 96%, 97%,         98%, or 99% of the polypeptide, first polypeptide, or second         polypeptide remains intact (e.g., greater than 600, 650, 700,         750, 800, 850, 900, 950, 1000, 1050, 1100, 1150, 1200, 1250,         1300, 1350, 1400, 1450, 1500, 1600, 1700, 1800, 1900, or 2000         amino acids long (and optionally, no larger than 2500, 2000,         1500, 1400, 1300, 1200, 1100, 1000, 900, 800, 700, or 600 amino         acids long)) after a stability test;     -   (xi) the potency of the polypeptide, first polypeptide, or         second polypeptide in a system for modifying DNA, e.g., whether         at least 1% of target sites are modified after a system         comprising the polypeptide, first polypeptide, or second         polypeptide is assayed for potency; or     -   (xii) the presence, absence, and/or level of one or more of a         pyrogen, virus, fungus, bacterial pathogen, or host cell         protein, e.g., whether the system is free or substantially free         of pyrogen, virus, fungus, bacterial pathogen, or host cell         protein contamination.

In some embodiments, a system or pharmaceutical composition described herein is endotoxin free.

In some embodiments, the presence, absence, and/or level of one or more of a pyrogen, virus, fungus, bacterial pathogen, and/or host cell protein is determined. In embodiments, whether the system is free or substantially free of pyrogen, virus, fungus, bacterial pathogen, and/or host cell protein contamination is determined.

In some embodiments, a pharmaceutical composition or system as described herein has one or more (e.g., 1, 2, 3, or 4) of the following characteristics:

-   -   (a) less than 1% (e.g., less than 0.5%, 0.4%, 0.3%, 0.2%, or         0.1%) DNA template relative to the template RNA and/or the RNA         encoding the polypeptide, e.g., on a molar basis;     -   (b) less than 1% (e.g., less than 0.5%, 0.4%, 0.3%, 0.2%, or         0.1%) uncapped RNA relative to the template RNA and/or the RNA         encoding the polypeptide, e.g., on a molar basis;     -   (c) less than 1% (e.g., less than 0.5%, 0.4%, 0.3%, 0.2%, or         0.1%) partial length RNAs relative to the template RNA and/or         the RNA encoding the polypeptide, e.g., on a molar basis;     -   (d) substantially lacks unreacted cap dinucleotides.

EXAMPLES Example 1: Quantifying Activity of a Gene Editing Polypeptide Using a GFP/BFP Assay in Human Cells

This example describes the use of gene modifying system containing an exemplary gene modifying polypeptide and an exemplary template RNA. In this example, the template RNA contains:

-   -   (1) a gRNA spacer;     -   (2) a gRNA scaffold;     -   (3) a heterologous object sequence; and     -   (4) a primer binding site (PBS) sequence.

More specifically, the template RNA comprises the following sequence:

(SEQ ID NO: 11,010) GCCGAAGCACTGCACGCCGTGTTTTAGAGCTAGAAATAG CAAGTTAAAATAAGGCTAGTCCGTTATCAACTTGAAAAA GTGGCACCGAGTCGGTGCACCCTGACGTACGGCGTGCA GTGCTT.

A gene modifying system comprising a given gene modifying polypeptide (e.g., one described herein) and the template RNA is transfected into the HEK293T BFP-expressing cell line. The gene modifying polypeptide and the template RNA are delivered by nucleofection in DNA format. Specifically, 800 ng of gene modifying polypeptide plasmid DNA is combined with 200 ng template RNA in plasmid format. The modifying polypeptide and template RNA in plasmid DNA format are added to 25 μL SF buffer containing 250,000 HEK293T BFP-expressing cells, and cells are nucleofected using program DS-150. After nucleofection, cells are grown at 37° C., 5% CO₂ for 3 days prior to cell lysis and genomic DNA extraction. To analyze gene editing activity, primers flanking the BFP locus can be used to amplify across the locus. Amplicons are analyzed via short read sequencing using an Illumina MiSeq. Conversion of the BFP gene sequence to the GFP gene sequence indicate successful editing. In some embodiments, the assay will indicate that at least 10%, 20%, 30%, 40%, 50%, 60%, or 70% of copies of the BFP gene in the sample are converted to the GFP gene.

Example 2: Gene Modifying Polypeptide Selection by Pooled Screening in HEK293T & U2OS Cells

This example describes the use of an RNA gene modifying system for the targeted editing of a coding sequence in the human genome. More specifically, this example describes the infection of HEK293T and U2OS cells with a library of gene modifying candidates, followed by transfection of a template guide RNA (tgRNA) for in vitro gene modifying in the cells, e.g., as a means of evaluating a new gene modifying polypeptide for editing activity in human cells by a pooled screening approach.

The gene modifying polypeptide library candidates assayed herein each comprise: 1) a Streptococcus pyogenes (S. pyogenes; Spy) Cas9 nickase containing an N863A mutation that inactivates one endonuclease active site; 2) one of the 122 peptide linkers depicted at Table 10; and 3) a reverse transcriptase (RT) domain from Table 6 of retroviral origin. The particular retroviral RT domains utilized were selected if they were expected to function as a monomer. For each selected RT domain, the wild-type sequences were tested, as well as versions with point mutations installed in the primary wild-type sequence. In particular, 143 RT domains were tested, either wild type or containing various mutations, based on exemplary RT domains listed in Table 2 (FIG. 2A). In total, 17,446 Cas-linker-RT gene modifying polypeptides (also referred to, in the context of the experiment, as individual elements or candidates) were tested. RT domains of the present disclosure can be grouped into families (each an “RT family”), each RT family comprising a wild type or reference RT sequence from a retrovirus and any variants of that RT wild type or reference sequence, e.g., RT sequences comprising one or more amino acid differences relative to the reference RT sequence. RT family candidates, accordingly, as used herein, refers to all gene modifying polypeptide candidates as described above, in which the RT sequence is selected from identified RT family.

The system described here is a two-component system comprising: 1) an expression plasmid encoding a human codon-optimized gene modifying polypeptide library candidate within a lentiviral cassette, and 2) a tgRNA expression plasmid expressing a non-coding tgRNA sequence that is recognized by Cas and localizes it to the genomic locus of interest, and that also templates reverse transcription of the desired edit into the genome by the RT domain, driven by a U6 promoter. The lentiviral cassette comprises: (i) a CMV promoter for expression in mammalian cells; (ii) a gene modifying polypeptide library candidate as shown; (iii) a self-cleaving T2A polypeptide; (iv) a puromycin resistance gene enabling selection in mammalian cells; and (v) a polyA tail termination signal.

To prepare a pool of cells expressing gene modifying polypeptide library candidates, HEK293T or U2OS cells were transduced with pooled lentiviral preparations of the gene modifying candidate plasmid library. HEK293 Lenti-X cells were seeded in 15 cm plates (12×10⁶ cells) prior to lentiviral plasmid transfection. Lentiviral plasmid transfection using the Lentiviral Packaging Mix (Biosettia, 27 ug) and the plasmid DNA for the gene modifying candidate library (27 ug) was performed the following day using Lipofectamine 2000 and Opti-MEM media according to the manufacturer's protocol. Extracellular DNA was removed by a full media change the next day and virus-containing media was harvested 48 hours after. Lentiviral media was concentrated using Lenti-X Concentrator (TaKaRa Biosciences) and 5 mL lentiviral aliquots were made and stored at −80° C. Lentiviral titering was performed by enumerating colony forming units post Puromycin selection. HEK293T or U2OS cells carrying a BFP-expressing genomic landing pad were seeded at 6×10⁷ cells in culture plates and transduced at a 0.3 multiplicity of infection (MOI) to minimize multiple infections per cell. Puromycin (2.5 ug/mL) was added 48 hours post infection to allow for selection of infected cells. Cells were kept under puromycin selection for at least 7 days and then scaled up for tgRNA electroporation.

To determine the genome-editing capacity of the gene modifying library candidates in the assay, infected BFP-expressing HEK293T or U2OS cells were then transfected by electroporation of 250,000 cells/well with 200 ng of a tgRNA (either g4 or g10) plasmid, designed to convert BFP to GFP, at sufficient cell count for >1000× coverage per library candidate.

The g4 tgRNA (5′ to 3′) is as follows: 20 nucleotide spacer region (GCCGAAGCACTGCACGCCGT; SEQ ID NO: 11,011), a scaffold region (GTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTG GCACCGAGTCGGTGC; SEQ ID NO: 11,012), the template region encoding the single base pair substitution to change BFP to GFP (bold) and a PAM inactivation that introduces a synonymous point mutation in the SpyCas9 PAM (NGG to NCG) that prevents re-engagement of the gene modifying polypeptide upon completion of a functional gene modifying reaction (underline) (ACCCTGACGTACG; SEQ ID NO: 11,013), and the 13 nucleotide PBS (GCGTGCAGTGCTT; SEQ ID NO: 11,014).

Similarly, the g10 tgRNA (5′ to 3′) is as follows: 20 nucleotide spacer region (AGAAGTCGTGCTGCTTCATG; SEQ ID NO: 11,015), a scaffold region (GTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTG GCACCGAGTCGGTGC; SEQ ID NO: 11,016), the template region encoding the single base pair substitution to change BFP to GFP (bold) and a PAM inactivation that introduces a synonymous point mutation in the SpyCas9 PAM (NGG to NGA) that prevents re-engagement of the gene modifying polypeptide upon completion of a functional gene modifying reaction (underline) (ACCCTGACCTACGGCGTGCAGTGCTTCGGCCGCTACCCCGATCACAT; SEQ ID NO: 11,017), and 13 nucleotide PBS (GAAGCAGCACGAC; SEQ ID NO: 11,018).

To assess the genome-editing capacity of the various constructs in the assay, cells were sorted by Fluorescence-Activated Cell Sorting (FACS) for GFP expression 6-7 days post-electroporation. Cells were sorted and harvested as distinct populations of unedited (BFP+) cells, edited (GFP+) cells and imperfect edit (BFP−, GFP−) cells (FIG. 3 ). A sample of unsorted cells was also harvested as the input population to determine enrichment during analysis.

To determine which gene modifying library candidates have genome-editing capacity in this assay, genomic DNA (gDNA) was harvested from sorted and unsorted cell populations, and analyzed by sequencing the gene modifying library candidates in each population. Briefly, gene modifying sequences were amplified from the genome using primers specific to the lentiviral cassette, amplified in a second round of PCR to dilute genomic DNA, and then sequenced using Oxford Nanopore Sequencing Technology according to the manufacturer's protocol.

After quality control of sequencing reads, reads of at least 1500 and no more than 3200 nucleotides were mapped to the gene modifying polypeptide library sequences and those containing a minimum of an 80% match to a library sequence were considered to be successfully aligned to a given candidate. To identify gene modifying candidates capable of performing gene editing in the assay, the read count of each library candidate in the edited population was compared to its read count in the initial, unsorted population. For purposes of this pooled screen, gene modifying candidates with genome-editing capacity were selected as those candidates that were enriched in the converted (GFP+) population relative to unsorted (input) cells and wherein the enrichment was determined to be at or above the enrichment level of a reference (Element ID No: 17380 as listed in Example 7).

A large number of gene modifying polypeptide candidates were determined to be enriched in the GFP+ cell populations. For example, of the 17,446 candidates tested, over 3,300 exhibited enrichment in GFP+ sorted populations (relative to unsorted) that was at least equivalent to that of the reference under similar experimental conditions (HEK293T using g4 tgRNA; HEK293T cells using g10 tgRNA; or U2OS cells using g4 tgRNA), shown in Table 1. Although the 17,446 candidates were also tested in U2OS cells using g10 tgRNA, the pooled screen did not yield candidates that were enriched in the converted (GFP+) population relative to unsorted (input) cells under that experimental condition. A subset of the gene modifying polypeptide candidates tested were selected for further analysis (amino acid sequences listed Table A1).

TABLE 1 Combinations of linker and RT sequences screened. The amino acid sequence of each RT in this table is provided in Table 6. SEQ ID NO: of Linker amino acid sequence Linker RT domain name EAAAKGSS 12,001 PERV_Q4VFZ2_3mutA_WS EAAAKEAAAKEAAAKEAAAK 12,002 MLVMS_P03355_PLV919 PAPEAAAK 12,003 MLVFF_P26809_3mutA EAAAKPAPGGG 12,004 MLVFF_P26809_3mutA GSSGSSGSSGSSGSSGSS 12,005 PERV_Q4VFZ2_3mut PAPGGGEAAAK 12,006 MLVAV_P03356_3mutA AEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKEAAAKA 12,007 MLVMS_P03355_PLV919 GSSEAAAK 12,008 MLVFF_P26809_3mutA EAAAKPAPGGS 12,009 MLVFF_P26809_3mutA GGSGGSGGSGGSGGSGGS 12,010 MLVFF_P26809_3mutA AEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKEAAAKA 12,011 XMRV6_A1Z651_3mutA AEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKEAAAKA 12,012 PERV_Q4VFZ2_3mutA_WS EAAAKEAAAKEAAAK 12,013 MLVFF_P26809_3mutA PAPEAAAKGSS 12,014 MLVFF_P26809_3mutA AEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKEAAAKA 12,015 PERV_Q4VFZ2_3mutA_WS EAAAKEAAAKEAAAK 12,016 PERV_Q4VFZ2_3mutA_WS AEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKEAAAKA 12,017 AVIRE_P03360_3mutA PAPAPAPAPAP 12,018 MLVCB_P08361_3mutA PAPAPAPAPAP 12,019 MLVFF_P26809_3mutA EAAAKGGSPAP 12,020 PERV_Q4VFZ2_3mutA_WS PAP MLVMS_P03355_PLV919 PAPGGGGSS 12,022 WMSV_P03359_3mutA SGSETPGTSESATPES 12,023 MLVFF_P26809_3mutA PAPEAAAKGSS 12,024 XMRV6_A1Z651_3mutA EAAAKGGSGGG 12,025 MLVMS_P03355_PLV919 GGGGSGGGGS 12,026 MLVFF_P26809_3mutA GGGPAPGSS 12,027 MLVAV_P03356_3mutA GGSGGSGGSGGSGGSGGS 12,028 XMRV6_A1Z651_3mut GGGGSGGGGSGGGGSGGGGSGGGGSGGGGS 12,029 MLVCB_P08361_3mutA GSSPAP 12,030 AVIRE_P03360_3mutA EAAAKGSSPAP 12,031 MLVFF_P26809_3mutA GSSGGGEAAAK 12,032 MLVFF_P26809_3mutA GGSGGSGGSGGSGGSGGS 12,033 MLVMS_P03355_3mutA_WS PAPAPAPAP 12,034 MLVFF_P26809_3mutA EAAAKEAAAKEAAAKEAAAK 12,035 XMRV6_A1Z651_3mutA EAAAKGGSPAP 12,036 MLVMS_P03355_3mutA_WS PAPGGSEAAAK 12,037 AVIRE_P03360_3mutA GGGGSGGGGSGGGGSGGGGSGGGGSGGGGS 12,038 AVIRE_P03360_3mutA EAAAKGGGGSEAAAK 12,039 MLVCB_P08361_3mutA AEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKEAAAKA 12,040 WMSV_P03359_3mutA GSS MLVMS_P03355_PLV919 GSSGSSGSSGSS 12,042 MLVMS_P03355_PLV919 GSSPAPEAAAK 12,043 XMRV6_A1Z651_3mutA GGSPAPEAAAK 12,044 MLVFF_P26809_3mutA GGGEAAAKGGS 12,045 MLVFF_P26809_3mutA EAAAKEAAAKEAAAKEAAAKEAAAK 12,046 PERV_Q4VFZ2_3mutA_WS GGGGGGGG 12,047 PERV_Q4VFZ2_3mut GGGPAP 12,048 MLVCB_P08361_3mutA PAPAPAPAPAPAP 12,049 MLVCB_P08361_3mutA GGSGGSGGSGGSGGSGGS 12,050 MLVCB_P08361_3mutA PAP MLVMS_P03355_3mutA_WS GGSGGSGGSGGSGGSGGS 12,052 PERV_Q4VFZ2_3mutA_WS PAPAPAPAPAPAP 12,053 MLVMS_P03355_PLV919 EAAAKPAPGSS 12,054 MLVMS_P03355_3mutA_WS EAAAKEAAAKEAAAKEAAAK 12,055 MLVMS_P03355_3mutA_WS EAAAKGGS 12,056 MLVMS_P03355_3mutA_WS GGGGSEAAAKGGGGS 12,057 MLVFF_P26809_3mutA EAAAKPAPGSS 12,058 MLVFF_P26809_3mutA GGGGSGGGGSGGGGSGGGGS 12,059 MLVMS_P03355_PLV919 EAAAKGGGGGS 12,060 MLVMS_P03355_PLV919 GGSPAP 12,061 XMRV6_A1Z651_3mutA EAAAKGGGPAP 12,062 MLVMS_P03355_PLV919 EAAAKEAAAKEAAAKEAAAKEAAAK 12,063 MLVFF_P26809_3mutA PAP MLVCB_P08361_3mutA EAAAK 12,065 XMRV6_A1Z651_3mutA GGSGSSPAP 12,066 PERV_Q4VFZ2_3mutA_WS GSSGSSGSSGSSGSSGSS 12,067 MLVMS_P03355_PLV919 GSSEAAAKGGG 12,068 MLVAV_P03356_3mutA GGGEAAAKGGS 12,069 XMRV6_A1Z651_3mutA EAAAKGGGGSEAAAK 12,070 MLVAV_P03356_3mutA GGGGSGGGGSGGGGS 12,071 MLVFF_P26809_3mutA GGGGSGGGGSGGGGSGGGGS 12,072 AVIRE_P03360_3mutA SGSETPGTSESATPES 12,073 AVIRE_P03360_3mutA GGGEAAAKPAP 12,074 MLVFF_P26809_3mutA EAAAKGSSGGG 12,075 MLVMS_P03355_3mutA_WS EAAAKEAAAKEAAAKEAAAKEAAAK 12,076 WMSV_P03359_3mut GGSGGSGGSGGS 12,077 XMRV6_A1Z651_3mutA GGSEAAAKPAP 12,078 MLVFF_P26809_3mutA EAAAKGSSGGG 12,079 XMRV6_A1Z651_3mutA GGGGS 12,080 MLVFF_P26809_3mutA GGGEAAAKGSS 12,081 MLVMS_P03355_PLV919 PAPAPAPAPAPAP 12,082 MLVAV_P03356_3mutA GGGGSGGGGSGGGGGGGGS 12,083 MLVCB_P08361_3mutA GGGEAAAKGSS 12,084 MLVCB_P08361_3mutA PAPGGSGSS 12,085 MLVFF_P26809_3mutA GSAGSAAGSGEF 12,086 MLVCB_P08361_3mutA PAPGGSEAAAK 12,087 MLVMS_P03355_3mutA_WS GGSGSS 12,088 XMRV6_A1Z651_3mutA PAPGGGGSS 12,089 MLVMS_P03355_PLV919 GSSGSSGSS 12,090 XMRV6_A1Z651_3mut AEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKEAAAKA 12,091 MLVMS_P03355_3mutA_WS EAAAK 12,092 MLVMS_P03355_PLV919 GSSGSSGSSGSS 12,093 MLVFF_P26809_3mutA PAPGGGGSS 12,094 MLVCB_P08361_3mutA GGGEAAAKGGS 12,095 MLVCB_P08361_3mutA PAPGGGEAAAK 12,096 MLVMS_P03355_PLV919 GGGGGSPAP 12,097 XMRV6_A1Z651_3mutA EAAAKGGS 12,098 XMRV6_A1Z651_3mutA EAAAKGSSPAP 12,099 XMRV6_A1Z651_3mut PAPEAAAK 12,100 MLVAV_P03356_3mutA GGSGGSGGSGGS 12,101 MLVMS_P03355_3mutA_WS GGGPAPGGS 12,102 MLVMS_P03355_PLV919 GSSGSSGSSGSS 12,103 PERV_Q4VFZ2_3mutA_WS EAAAKPAPGGS 12,104 MLVCB_P08361_3mutA GSSGSS 12,105 MLVFF_P26809_3mutA EAAAKEAAAKEAAAKEAAAK 12,106 MLVCB_P08361_3mutA EAAAKEAAAKEAAAKEAAAK 12,107 FLV_P10273_3mutA GSS MLVFF_P26809_3mutA EAAAKEAAAK 12,109 MLVMS_P03355_3mutA_WS PAPEAAAKGGG 12,110 MLVAV_P03356_3mutA GGSGSSEAAAK 12,111 MLVFF_P26809_3mutA EAAAKEAAAKEAAAKEAAAKEAAAK 12,112 PERV_Q4VFZ2 GSSEAAAKPAP 12,113 AVIRE_P03360_3mutA EAAAKEAAAKEAAAKEAAAKEAAAK 12,114 MLVCB_P08361_3mutA EAAAKGGG 12,115 MLVFF_P26809_3mutA GSSPAPGGG 12,116 MLVCB_P08361_3mutA GGGPAPGSS 12,117 MLVMS_P03355_PLV919 GGGGGS 12,118 MLVMS_P03355_3mutA_WS EAAAKEAAAKEAAAKEAAAKEAAAKEAAAK 12,119 PERV_Q4VFZ2_3mut GGGGSGGGGSGGGGSGGGGSGGGGS 12,120 WMSV_P03359_3mutA EAAAKEAAAKEAAAK 12,121 PERV_Q4VFZ2_3mut PAPAPAPAP 12,122 MLVCB_P08361_3mutA GSSGSSGSSGSSGSS 12,123 PERV_Q4VFZ2_3mut GGGGSSEAAAK 12,124 MLVMS_P03355_3mutA_WS GGSGGSGGSGGS 12,125 MLVCB_P08361_3mutA PAPEAAAKGGS 12,126 MLVCB_P08361_3mutA EAAAKEAAAKEAAAKEAAAKEAAAKEAAAK 12,127 MLVCB_P08361_3mutA EAAAKGGGGSEAAAK 12,128 MLVMS_P03355_PLV919 EAAAKGGGGSEAAAK 12,129 MLVMS_P03355_3mutA_WS EAAAKGGGPAP 12,130 XMRV6_A1Z651_3mut EAAAKEAAAKEAAAKEAAAKEAAAK 12,131 MLVMS_P03355_3mutA_WS AEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKEAAAKA 12,132 FLV_P10273_3mutA GGSEAAAKGGG 12,133 MLVMS_P03355_3mutA_WS GGGGSGGGGSGGGGSGGGGSGGGGSGGGGS 12,134 KORV_Q9TTC1-Pro_3mutA GGGPAPGGS 12,135 MLVCB_P08361_3mutA PAPAPAPAPAPAP 12,136 XMRV6_A1Z651_3mutA GGSGSSGGG 12,137 XMRV6_A1Z651_3mutA GGSGSSGGG 12,138 MLVCB_P08361_3mutA GGGEAAAKGGS 12,139 MLVMS_P03355_3mutA_WS EAAAK 12,140 MLVCB_P08361_3mutA GGSPAPGSS 12,141 MLVMS_P03355_3mutA_WS GGGGSSEAAAK 12,142 PERV_Q4VFZ2_3mut PAPAPAPAPAP 12,143 MLVBM_Q7SVK7_3mut EAAAKEAAAKEAAAKEAAAK 12,144 MLVAV_P03356_3mutA GGGGGSGSS 12,145 MLVCB_P08361_3mutA EAAAKGSSPAP 12,146 MLVMS_P03355_3mutA_WS PAPAPAPAPAPAP 12,147 MLVMS_P03355_3mutA_WS GSSGGGGGS 12,148 MLVMS_P03355_3mutA_WS PAPGSSGGG 12,149 MLVMS_P03355_PLV919 GGSGGGPAP 12,150 MLVCB_P08361_3mutA GGGGGGG 12,151 MLVCB_P08361_3mutA GSSGSSGSSGSSGSSGSS 12,152 MLVCB_P08361_3mutA GGGPAPGGS 12,153 MLVFF_P26809_3mutA EAAAKGGSGGG 12,154 PERV_Q4VFZ2_3mut EAAAKGGGGSS 12,155 MLVMS_P03355_3mutA_WS GSSGSSGSSGSSGSSGSS 12,156 MLVMS_P03355_3mut GGGGSGGGGSGGGGSGGGGS 12,157 MLVBM_Q7SVK7_3mutA_WS PAPAPAPAPAP 12,158 MLVMS_P03355_PLV919 GGGEAAAKGGS 12,159 MLVMS_P03355_PLV919 AEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKEAAAKA 12,160 MLVMS_P03355_3mut GSAGSAAGSGEF 12,161 MLVMS_P03355_3mutA_WS GSSGSSGSSGSSGSS 12,162 MLVFF_P26809_3mutA EAAAKGGSGSS 12,163 MLVFF_P26809_3mutA PAPGGG 12,164 MLVFF_P26809_3mutA GGGPAPGSS 12,165 XMRV6_A1Z651_3mutA PAPEAAAKGGS 12,166 AVIRE_P03360_3mutA PAPGGGEAAAK 12,167 MLVFF_P26809_3mut GGGGSSEAAAK 12,168 MLVCB_P08361_3mutA EAAAK 12,169 MLVMS_P03355_PLV919 GGGGSGGGGSGGGGSGGGGSGGGGSGGGGS 12,170 BAEVM_P10272_3mutA GGSGGGEAAAK 12,171 MLVMS_P03355_PLV919 AEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKEAAAKA 12,172 MLVFF_P26809_3mutA GSSPAPGGS 12,173 XMRV6_A1Z651_3mutA GGSGGGPAP 12,174 MLVMS_P03355_PLV919 EAAAK 12,175 AVIRE_P03360_3mutA GSS XMRV6_A1Z651_3mutA GGSGGSGGS 12,177 MLVFF_P26809_3mutA EAAAKEAAAKEAAAKEAAAK 12,178 AVIRE_P03360_3mut PAPEAAAKGGG 12,179 PERV_Q4VFZ2_3mutA_WS GGGGGSEAAAK 12,180 BAEVM_P10272_3mutA GGSGSSGGG 12,181 MLVMS_P03355_3mutA_WS GGGGGGG 12,182 MLVMS_P03355_3mutA_WS GSSEAAAKPAP 12,183 PERV_Q4VFZ2_3mut GGGGGSEAAAK 12,184 WMSV_P03359_3mut GGGGSGGGGSGGGGSGGGGSGGGGS 12,185 MLVFF_P26809_3mut GGGEAAAKGGS 12,186 AVIRE_P03360_3mutA GGSPAPGGG 12,187 AVIRE_P03360_3mutA GSAGSAAGSGEF 12,188 MLVAV_P03356_3mutA EAAAK 12,189 MLVAV_P03356_3mutA EAAAKPAPGSS 12,190 WMSV_P03359_3mutA EAAAKEAAAKEAAAKEAAAKEAAAKEAAAK 12,191 PERV_Q4VFZ2_3mutA_WS GGSEAAAKPAP 12,192 MLVCB_P08361_3mutA PAPAPAPAPAPAP 12,193 MLVBM_Q7SVK7_3mutA_WS GGSPAPGGG 12,194 MLVMS_P03355_3mutA_WS GGSEAAAKGGG 12,195 MLVMS_P03355_3mut GGSGGSGGSGGS 12,196 MLVFF_P26809_3mutA EAAAKEAAAKEAAAKEAAAKEAAAKEAAAK 12,197 MLVFF_P26809_3mutA GGG AVIRE_P03360_3mutA AEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKEAAAKA 12,199 PERV_Q4VFZ2_3mut GGSGGSGGSGGS 12,200 MLVMS_P03355_3mutA_WS GGGEAAAK 12,201 MLVCB_P08361_3mutA GSSGSSGSSGSSGSSGSS 12,202 MLVMS_P03355_3mutA_WS GSSGGGPAP 12,203 MLVMS_P03355_3mutA_WS GSSEAAAKPAP 12,204 MLVFF_P26809_3mutA EAAAKEAAAK 12,205 MLVMS_P03355_PLV919 GGGGSGGGGSGGGGSGGGGSGGGGSGGGGS 12,206 MLVCB_P08361_3mut GGGGGG 12,207 MLVMS_P03355_3mutA_WS GGSGSSGGG 12,208 MLVFF_P26809_3mutA GSSGGGEAAAK 12,209 PERV_Q4VFZ2_3mutA_WS PAPAPAPAPAP 12,210 PERV_Q4VFZ2_3mut EAAAKEAAAKEAAAKEAAAKEAAAKEAAAK 12,211 SFV3L_P27401_2mut EAAAKGGSGGG 12,212 BAEVM_P10272_3mutA GGGGSSPAP 12,213 PERV_Q4VFZ2_3mutA_WS GGGEAAAKPAP 12,214 MLVMS_P03355_PLV919 GGSGGGPAP 12,215 BAEVM_P10272_3mutA PAPGSSGGS 12,216 MLVMS_P03355_PLV919 GGSGGGPAP 12,217 MLVMS_P03355_3mutA_WS EAAAKGGSPAP 12,218 PERV_Q4VFZ2_3mutA_WS EAAAKGGSGGG 12,219 MLVMS_P03355_3mutA_WS PAPGSSGGG 12,220 MLVFF_P26809_3mutA GSSEAAAKGGS 12,221 MLVFF_P26809_3mutA PAPGSSEAAAK 12,222 MLVFF_P26809_3mutA EAAAKGSSPAP 12,223 KORV_Q9TTC1-Pro_3mutA EAAAKEAAAKEAAAKEAAAKEAAAK 12,224 MLVBM_Q7SVK7_3mutA_WS PAPGSSEAAAK 12,225 MLVMS_P03355_PLV919 EAAAKGSSGGG 12,226 MLVMS_P03355_3mutA_WS EAAAKGGGGGS 12,227 AVIRE_P03360_3mutA EAAAKEAAAKEAAAK 12,228 MLVMS_P03355_PLV919 PAPAPAPAPAPAP 12,229 MLVFF_P26809_3mutA GGGGSGGGGSGGGGS 12,230 MLVCB_P08361_3mutA PAPGGSEAAAK 12,231 MLVCB_P08361_3mutA PAPGSSEAAAK 12,232 MLVBM_Q7SVK7_3mutA_WS PAPEAAAKGSS 12,233 AVIRE_P03360_3mutA GGSPAPGSS 12,234 WMSV_P03359_3mutA PAPGGSGGG 12,235 MLVMS_P03355_PLV919 EAAAKGGSGSS 12,236 MLVMS_P03355_3mutA_WS GGSGGG 12,237 MLVFF_P26809_3mutA GGSEAAAKGSS 12,238 KORV_Q9TTC1_3mutA AEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKEAAAKA 12,239 MLVCB_P08361_3mutA PAPAPAPAPAPAP 12,240 PERV_Q4VFZ2_3mutA_WS PAPEAAAK 12,241 MLVMS_P03355_3mutA_WS GGSEAAAKGGG 12,242 MLVMS_P03355_PLV919 GSSPAP 12,243 MLVMS_P03355_3mutA_WS GGGGSS 12,244 MLVMS_P03355_PLV919 GGGEAAAKPAP 12,245 AVIRE_P03360_3mutA EAAAKPAPGGS 12,246 MLVAV_P03356_3mutA EAAAKGGGPAP 12,247 MLVAV_P03356_3mutA PAPGGSEAAAK 12,248 BAEVM_P10272_3mutA PAPGGSGSS 12,249 MLVMS_P03355_3mutA_WS PAPGGSGSS 12,250 AVIRE_P03360_3mutA GGSGGGPAP 12,251 MLVMS_P03355_3mutA_WS EAAAKEAAAKEAAAKEAAAK 12,252 BAEVM_P10272_3mutA GGGGSGGGGSGGGGSGGGGSGGGGS 12,253 MLVMS_P03355_PLV919 GGGGSSPAP 12,254 MLVCB_P08361_3mutA GSSGGGPAP 12,255 MLVFF_P26809_3mutA GGGGSSGGS 12,256 MLVMS_P03355_PLV919 GGSGGG 12,257 MLVCB_P08361_3mutA GSSGGGGGS 12,258 MLVMS_P03355_PLV919 SGGSSGGSSGSETPGTSESATPESSGGSSGGSS 12,259 XMRV6_A1Z651_3mutA GGGGGSGSS 12,260 KORV_Q9TTC1_3mut GGGEAAAKGGS 12,261 BAEVM_P10272_3mutA GGSGGG 12,262 BAEVM_P10272_3mutA PAPAPAP 12,263 KORV_Q9TTC1-Pro_3mut AEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKEAAAKA 12,264 SFV3L_P27401_2mutA AEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKEAAAKA 12,265 MLVBM_Q7SVK7_3mutA_WS GSSGSSGSSGSSGSS 12,266 MLVMS_P03355_3mutA_WS GSSGGGEAAAK 12,267 MLVMS_P03355_3mutA_WS GSSGGSEAAAK 12,268 MLVFF_P26809_3mutA PAP MLVMS_P03355_PLV919 EAAAKGGGGSEAAAK 12,270 MLVBM_Q7SVK7_3mutA_WS PAPAP 12,271 AVIRE_P03360_3mutA PAP MLVFF_P26809_3mutA GSSGGG 12,273 MLVMS_P03355_3mut GSSPAPGGS 12,274 MLVFF_P26809_3mutA PAPAPAPAP 12,275 XMRV6_A1Z651_3mutA EAAAKGSSGGS 12,276 PERV_Q4VFZ2_3mut PAPEAAAKGGG 12,277 KORV_Q9TTC1-Pro_3mutA PAPGGS 12,278 MLVCB_P08361_3mutA EAAAKGGG 12,279 MLVCB_P08361_3mutA GSSEAAAKPAP 12,280 MLVMS_P03355_PLV919 PAPGGS 12,281 MLVFF_P26809_3mutA EAAAKGGS 12,282 MLVCB_P08361_3mutA EAAAKEAAAKEAAAKEAAAKEAAAKEAAAK 12,283 FLV_P10273_3mutA PAPGGSEAAAK 12,284 MLVAV_P03356_3mutA GSS MLVCB_P08361_3mutA GSSGSSGSSGSS 12,286 AVIRE_P03360_3mutA GSSGSSGSS 12,287 MLVFF_P26809_3mutA GSSGGG 12,288 MLVMS_P03355_PLV919 EAAAK 12,289 MLVFF_P26809_3mutA GGSPAPEAAAK 12,290 MLVCB_P08361_3mutA GGSGSS 12,291 MLVCB_P08361_3mutA GSSPAPGGG 12,292 MLVMS_P03355_PLV919 EAAAKEAAAKEAAAKEAAAKEAAAK 12,293 MLVAV_P03356_3mutA EAAAKGSSPAP 12,294 FLV_P10273_3mutA GGGGSS 12,295 XMRV6_A1Z651_3mutA GGSPAPGSS 12,296 MLVMS_P03355_PLV919 EAAAKEAAAKEAAAKEAAAKEAAAK 12,297 MLVMS_P03355_3mutA_WS PAPEAAAKGGG 12,298 FLV_P10273_3mutA EAAAKPAPGGS 12,299 XMRV6_A1Z651_3mut PAPAP 12,300 BAEVM_P10272_3mutA EAAAKEAAAKEAAAKEAAAK 12,301 MLVMS_P03355_PLV919 GSSPAPGGG 12,302 MLVMS_P03355_PLV919 EAAAKGGGPAP 12,303 KORV_Q9TTC1_3mutA PAPEAAAK 12,304 MLVMS_P03355_PLV919 PAPGGGEAAAK 12,305 PERV_Q4VFZ2_3mutA_WS EAAAKGSSGGS 12,306 MLVMS_P03355_3mutA_WS EAAAKEAAAKEAAAK 12,307 MLVMS_P03355_PLV919 GSSEAAAK 12,308 MLVMS_P03355_3mutA_WS GSSGSSGSSGSS 12,309 MLVMS_P03355_3mutA_WS GGGGSGGGGSGGGGSGGGGS 12,310 MLVMS_P03355_3mutA_WS EAAAKGGGGSEAAAK 12,311 MLVMS_P03355_3mut GGS MLVCB_P08361_3mutA GGGGSGGGGSGGGGSGGGGSGGGGSGGGGS 12,313 XMRV6_A1Z651_3mutA GGSGSSPAP 12,314 MLVCB_P08361_3mutA GGGGGGGGSGGGGS 12,315 XMRV6_A1Z651_3mutA PAPAPAPAPAP 12,316 BAEVM_P10272_3mutA PAPAPAPAPAP 12,317 MLVMS_P03355_3mutA_WS EAAAKEAAAKEAAAKEAAAK 12,318 MLVBM_Q7SVK7_3mut GGGGSGGGGSGGGGSGGGGSGGGGS 12,319 BAEVM_P10272_3mutA GGSGGSGGS 12,320 MLVMS_P03355_3mutA_WS EAAAKPAPGSS 12,321 MLVMS_P03355_PLV919 GSS MLVMS_P03355_3mutA_WS PAPEAAAKGGS 12,323 MLVMS_P03355_3mutA_WS GGGPAPGGS 12,324 MLVMS_P03355_3mutA_WS EAAAKGGGGSS 12,325 MLVAV_P03356_3mutA GSSGSSGSSGSSGSS 12,326 MLVFF_P26809_3mut SGSETPGTSESATPES 12,327 PERV_Q4VFZ2_3mut GGSEAAAKGGG 12,328 MLVMS_P03355_3mut GSSGSSGSSGSSGSSGSS 12,329 AVIRE_P03360_3mutA PAPAPAPAPAPAP 12,330 AVIRE_P03360_3mut GGSGGS 12,331 XMRV6_A1Z651_3mutA PAPGSSEAAAK 12,332 MLVCB_P08361_3mut GGSPAPEAAAK 12,333 PERV_Q4VFZ2_3mut EAAAKGGGGGS 12,334 MLVCB_P08361_3mutA GGSGGSGGSGGS 12,335 MLVMS_P03355_PLV919 GGGGSSEAAAK 12,336 MLVMS_P03355_PLV919 GSSEAAAKGGG 12,337 MLVFF_P26809_3mutA PAPGGS 12,338 MLVMS_P03355_3mutA_WS EAAAKGGSGGG 12,339 MLVCB_P08361_3mutA EAAAKGGG 12,340 PERV_Q4VFZ2_3mut PAPGGS 12,341 XMRV6_A1Z651_3mutA GSSPAPGGG 12,342 XMRV6_A1Z651_3mutA PAPEAAAKGGG 12,343 MLVMS_P03355_3mutA_WS GSSEAAAKGGG 12,344 PERV_Q4VFZ2_3mutA_WS PAPGGSEAAAK 12,345 XMRV6_A1Z651_3mutA GGGGGS 12,346 MLVMS_P03355_3mutA_WS GGSPAPEAAAK 12,347 MLVMS_P03355_3mutA_WS GGGPAP 12,348 MLVFF_P26809_3mutA PAPGSSGGG 12,349 XMRV6_A1Z651_3mutA PAPGSSGGG 12,350 MLVBM_Q7SVK7_3mutA_WS GGGEAAAKGSS 12,351 MLVMS_P03355_3mutA_WS GSSEAAAKGGS 12,352 MLVCB_P08361_3mutA PAPGGSGSS 12,353 MLVCB_P08361_3mutA EAAAKGGGGSEAAAK 12,354 BAEVM_P10272_3mutA PAPAPAP 12,355 PERV_Q4VFZ2_3mutA_WS GGGGGG 12,356 MLVAV_P03356_3mutA GSSPAPEAAAK 12,357 MLVCB_P08361_3mutA GGSGGSGGS 12,358 MLVMS_P03355_3mutA_WS GSSGSSGSSGSSGSS 12,359 XMRV6_A1Z651_3mut GGGPAPGGS 12,360 XMRV6_A1Z651_3mutA GGGPAPEAAAK 12,361 BAEVM_P10272_3mutA GGSGGG 12,362 AVIRE_P03360_3mutA SGSETPGTSESATPES 12,363 PERV_Q4VFZ2_3mutA_WS EAAAKGSSPAP 12,364 MLVMS_P03355_PLV919 GSSEAAAK 12,365 XMRV6_A1Z651_3mut GSSGGSGGG 12,366 MLVFF_P26809_3mutA EAAAKEAAAKEAAAKEAAAKEAAAK 12,367 WMSV_P03359_3mutA GGGGSEAAAKGGGGS 12,368 MLVMS_P03355_PLV919 PAPGGGGSS 12,369 MLVMS_P03355_3mutA_WS SGSETPGTSESATPES 12,370 MLVMS_P03355_3mutA_WS GGSPAPEAAAK 12,371 KORV_Q9TTC1-Pro_3mutA GSSEAAAKGGG 12,372 MLVMS_P03355_3mutA_WS GSSEAAAK 12,373 WMSV_P03359_3mutA GGGGSEAAAKGGGGS 12,374 AVIRE_P03360_3mutA GSS WMSV_P03359_3mutA PAPGGSEAAAK 12,376 MLVFF_P26809_3mutA GGGGS 12,377 MLVMS_P03355_3mutA_WS GGGPAP 12,378 MLVMS_P03355_3mutA_WS EAAAKEAAAKEAAAKEAAAKEAAAKEAAAK 12,379 MLVMS_P03355_3mutA_WS EAAAKPAPGSS 12,380 PERV_Q4VFZ2_3mut EAAAKPAPGSS 12,381 MLVCB_P08361_3mutA GGGGGG 12,382 WMSV_P03359_3mutA EAAAKPAPGGS 12,383 MLVMS_P03355_PLV919 PAPGGGEAAAK 12,384 PERV_Q4VFZ2_3mut EAAAKEAAAKEAAAKEAAAKEAAAK 12,385 AVIRE_P03360_3mutA GSSEAAAKPAP 12,386 XMRV6_A1Z651_3mutA PAPGGSEAAAK 12,387 MLVBM_Q7SVK7_3mutA_WS PAPGSS 12,388 MLVCB_P08361_3mutA EAAAKGGG 12,389 MLVMS_P03355_3mutA_WS EAAAKPAP 12,390 MLVCB_P08361_3mutA PAPEAAAKGGS 12,391 MLVBM_Q7SVK7_3mutA_WS GGSPAPGGG 12,392 MLVCB_P08361_3mutA PAPGGSGSS 12,393 WMSV_P03359_3mutA EAAAKEAAAKEAAAKEAAAKEAAAKEAAAK 12,394 MLVMS_P03355_PLV919 GGSGGGPAP 12,395 MLVMS_P03355_PLV919 AEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKEAAAKA 12,396 MLVMS_P03355 PAPEAAAKGSS 12,397 MLVCB_P08361_3mutA EAAAKGSS 12,398 MLVMS_P03355_3mutA_WS GGSGGS 12,399 MLVMS_P03355_3mutA_WS EAAAKEAAAKEAAAKEAAAKEAAAK 12,400 BAEVM_P10272_3mutA GGGGSEAAAKGGGGS 12,401 FLV_P10273_3mutA GGSEAAAKGGG 12,402 MLVCB_P08361_3mutA GSSGSSGSSGSSGSS 12,403 BAEVM_P10272_3mutA GGGGSGGGGSGGGGSGGGGSGGGGSGGGGS 12,404 MLVFF_P26809_3mutA EAAAKGGG 12,405 PERV_Q4VFZ2_3mut GGGGGSEAAAK 12,406 MLVCB_P08361_3mutA EAAAKPAPGGS 12,407 MLVMS_P03355_3mutA_WS GGGGGSGSS 12,408 XMRV6_A1Z651_3mutA PAPGSSEAAAK 12,409 MLVMS_P03355_3mutA_WS GSSEAAAKPAP 12,410 MLVCB_P08361_3mutA EAAAKGSSPAP 12,411 MLVAV_P03356_3mutA GGGPAPGGS 12,412 WMSV_P03359_3mutA GGSPAP 12,413 MLVMS_P03355_3mutA_WS GGSEAAAKGGG 12,414 MLVMS_P03355_3mutA_WS GGGGGGGG 12,415 MLVFF_P26809_3mutA GGGGSGGGGSGGGGSGGGGSGGGGSGGGGS 12,416 MLVMS_P03355_3mutA_WS GGGGSGGGGSGGGGSGGGGSGGGGSGGGGS 12,417 MLVBM_Q7SVK7_3mutA_WS GSSPAPGGG 12,418 MLVAV_P03356_3mutA GGGGGG 12,419 AVIRE_P03360_3mutA GSSGGS 12,420 MLVMS_P03355_3mutA_WS GGSPAPGSS 12,421 MLVFF_P26809_3mutA PAPEAAAKGGG 12,422 PERV_Q4VFZ2_3mut EAAAKGGGPAP 12,423 MLVFF_P26809_3mutA GGGEAAAKGGS 12,424 MLVMS_P03355_PLV919 GGSGSSPAP 12,425 MLVFF_P26809_3mutA SGSETPGTSESATPES 12,426 WMSV_P03359_3mutA PAPGGSEAAAK 12,427 MLVBM_Q7SVK7_3mutA_WS GGSGGG 12,428 MLVMS_P03355_PLV919 GGGGSSPAP 12,429 PERV_Q4VFZ2_3mut GGGEAAAKGSS 12,430 MLVAV_P03356_3mutA PAPAPAPAPAPAP 12,431 MLVMS_P03355_3mutA_WS EAAAKGGGGSEAAAK 12,432 PERV_Q4VFZ2 EAAAKEAAAKEAAAKEAAAKEAAAK 12,433 MLVMS_P03355_PLV919 GGGGGSEAAAK 12,434 PERV_Q4VFZ2_3mut PAPGSSEAAAK 12,435 MLVCB_P08361_3mutA GSAGSAAGSGEF 12,436 PERV_Q4VFZ2_3mutA_WS EAAAKGGGGSEAAAK 12,437 MLVFF_P26809_3mutA GGSPAPGGG 12,438 PERV_Q4VFZ2_3mutA_WS GSSEAAAKGGG 12,439 AVIRE_P03360_3mutA GGGEAAAKPAP 12,440 MLVMS_P03355_3mutA_WS GGGPAP 12,441 AVIRE_P03360_3mutA GGSEAAAK 12,442 MLVCB_P08361_3mutA SGGSSGGSSGSETPGTSESATPESSGGSSGGSS 12,443 PERV_Q4VFZ2_3mut EAAAKPAPGGS 12,444 MLVBM_Q7SVK7_3mutA_WS AEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKEAAAKA 12,445 XMRV6_A1Z651_3mut GGGGGGGG 12,446 MLVCB_P08361_3mutA PAPGSS 12,447 PERV_Q4VFZ2_3mut EAAAK 12,448 PERV_Q4VFZ2_3mut GSAGSAAGSGEF 12,449 MLVMS_P03355_3mutA_WS PAPGGGEAAAK 12,450 PERV_Q4VFZ2_3mut EAAAKGSSGGS 12,451 MLVFF_P26809_3mut GGGGSEAAAKGGGGS 12,452 BAEVM_P10272_3mutA GGGGSGGGGSGGGGS 12,453 MLVMS_P03355_PLV919 EAAAKGGGGSEAAAK 12,454 BAEVM_P10272_3mut PAPGGGEAAAK 12,455 MLVMS_P03355_3mutA_WS GGSEAAAKPAP 12,456 MLVMS_P03355_3mutA_WS PAPAP 12,457 MLVCB_P08361_3mutA PAPAP 12,458 MLVFF_P26809_3mutA GGSPAP 12,459 AVIRE_P03360_3mutA EAAAKGSSGGS 12,460 MLVCB_P08361_3mutA PAPGSSGGS 12,461 AVIRE_P03360_3mutA EAAAKGGGGSEAAAK 12,462 XMRV6_A1Z651_3mutA PAPAPAP 12,463 BAEVM_P10272_3mutA GGSGGSGGSGGSGGSGGS 12,464 MLVMS_P03355_PLV919 GGGGGSGSS 12,465 MLVMS_P03355_PLV919 PAPGSSEAAAK 12,466 XMRV6_A1Z651_3mut GGSEAAAKPAP 12,467 XMRV6_A1Z651_3mutA EAAAKEAAAKEAAAKEAAAK 12,468 XMRV6_A1Z651_3mut AEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKEAAAKA 12,469 WMSV_P03359_3mut GGSGGGEAAAK 12,470 XMRV6_A1Z651_3mutA GGGEAAAK 12,471 XMRV6_A1Z651_3mutA GGGGSGGGGSGGGGS 12,472 MLVMS_P03355_3mutA_WS GGSGGSGGSGGSGGS 12,473 MLVFF_P26809_3mutA GSSGGGGGS 12,474 MLVMS_P03355_3mut PAPGGSEAAAK 12,475 MLVMS_P03355_3mutA_WS GSSGGSPAP 12,476 MLVMS_P03355_3mutA_WS SGSETPGTSESATPES 12,477 XMRV6_A1Z651_3mutA GGGGSGGGGS 12,478 MLVMS_P03355_PLV919 PAPAPAPAPAP 12,479 MLVMS_P03355_3mut GSSGSS 12,480 XMRV6_A1Z651_3mutA GSSEAAAKPAP 12,481 PERV_Q4VFZ2_3mut GGSGSSGGG 12,482 MLVMS_P03355_3mutA_WS EAAAKEAAAK 12,483 MLVCB_P08361_3mutA GSSGSSGSSGSS 12,484 MLVMS_P03355_3mutA_WS GSSPAPGGG 12,485 PERV_Q4VFZ2_3mutA_WS EAAAKEAAAKEAAAK 12,486 MLVMS_P03355_3mutA_WS AEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKEAAAKA 12,487 SFV1_P23074_2mutA GGGGSGGGGSGGGGSGGGGSGGGGSGGGGS 12,488 MLVMS_P03355_PLV919 GSAGSAAGSGEF 12,489 MLVMS_P03355_PLV919 PAPGSSEAAAK 12,490 MLVMS_P03355_3mutA_WS GGSEAAAK 12,491 MLVMS_P03355_3mutA_WS GSSGSSGSSGSSGSS 12,492 PERV_Q4VFZ2_3mutA_WS GGSEAAAKPAP 12,493 PERV_Q4VFZ2_3mutA_WS GGSGGSGGS 12,494 MLVCB_P08361_3mutA EAAAKGGSGSS 12,495 MLVCB_P08361_3mutA GGGGSGGGGSGGGGSGGGGSGGGGS 12,496 FLV_P10273_3mutA EAAAKEAAAKEAAAKEAAAK 12,497 MLVBM_Q7SVK7_3mutA_WS GGSGSSPAP 12,498 BAEVM_P10272_3mutA EAAAKEAAAKEAAAKEAAAKEAAAK 12,499 XMRV6_A1Z651_3mutA GGGGSGGGGSGGGGSGGGGSGGGGS 12,500 MLVBM_Q7SVK7_3mutA_WS GGSGSS 12,501 WMSV_P03359_3mutA PAPEAAAK 12,502 MLVCB_P08361_3mutA EAAAKPAP 12,503 BAEVM_P10272_3mutA GSSPAP 12,504 PERV_Q4VFZ2_3mutA_WS GGGPAP 12,505 PERV_Q4VFZ2_3mutA_WS EAAAKGGSGSS 12,506 MLVMS_P03355_3mutA_WS EAAAKGGGGSEAAAK 12,507 AVIRE_P03360_3mutA GGSGGG 12,508 KORV_Q9TTC1-Pro_3mutA GSSPAP 12,509 MLVFF_P26809_3mutA GGSGSSEAAAK 12,510 BAEVM_P10272_3mutA PAPGSSGGS 12,511 BAEVM_P10272_3mutA GGGGGG 12,512 MLVFF_P26809_3mutA PAPGGSEAAAK 12,513 MLVMS_P03355_PLV919 PAPGGS 12,514 MLVMS_P03355_PLV919 GGSGGSGGSGGS 12,515 BAEVM_P10272_3mutA GSSPAP 12,516 MLVCB_P08361_3mutA PAPAPAPAP 12,517 MLVMS_P03355_3mutA_WS GGGGGG 12,518 MLVCB_P08361_3mutA GSSGSSGSSGSSGSSGSS 12,519 KORV_Q9TTC1-Pro_3mutA GSSEAAAKGGS 12,520 BAEVM_P10272_3mutA GGSEAAAK 12,521 FLV_P10273_3mutA GGSGGSGGSGGSGGS 12,522 KORV_Q9TTC1-Pro_3mutA GSSPAPEAAAK 12,523 PERV_Q4VFZ2_3mut GSSGSSGSSGSSGSS 12,524 XMRV6_A1Z651_3mutA EAAAKPAPGGS 12,525 MLVMS_P03355_3mut SGGSSGGSSGSETPGTSESATPESSGGSSGGSS 12,526 FLV_P10273_3mut GGSPAPEAAAK 12,527 XMRV6_A1Z651_3mut EAAAKGGSGGG 12,528 MLVFF_P26809_3mutA EAAAKEAAAKEAAAKEAAAK 12,529 MLVFF_P26809_3mutA GSSPAP 12,530 WMSV_P03359_3mutA PAPAPAPAP 12,531 MLVAV_P03356_3mutA PAPGGSEAAAK 12,532 KORV_Q9TTC1_3mut GGSGSSEAAAK 12,533 MLVBM_Q7SVK7_3mutA_WS GSSGGG 12,534 MLVCB_P08361_3mutA GGGEAAAKGSS 12,535 PERV_Q4VFZ2_3mut PAPGGSGGG 12,536 MLVFF_P26809_3mutA AEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKEAAAKA 12,537 FFV_093209 PAPGGGGSS 12,538 MLVMS_P03355_3mutA_WS EAAAKGGS 12,539 MLVAV_P03356_3mutA EAAAKEAAAKEAAAKEAAAKEAAAKEAAAK 12,540 MLVBM_Q7SVK7_3mutA_WS GGSGGSGGS 12,541 WMSV_P03359_3mutA PAPAP 12,542 MLVMS_P03355_3mutA_WS GSSGGGEAAAK 12,543 MLVAV_P03356_3mutA GGGGSSEAAAK 12,544 MLVFF_P26809_3mutA EAAAKGSSGGS 12,545 MLVMS_P03355_PLV919 EAAAKGGGGSEAAAK 12,546 MLVMS_P03355_3mutA_WS GGGGGGGG 12,547 MLVMS_P03355_PLV919 GSSGSSGSS 12,548 MLVMS_P03355_PLV919 GGGEAAAKPAP 12,549 PERV_Q4VFZ2_3mutA_WS GGGGGSGSS 12,550 MLVMS_P03355_3mutA_WS GGGGGGG 12,551 MLVMS_P03355_PLV919 GGS MLVMS_P03355_PLV919 GSSGGG 12,553 MLVMS_P03355_3mutA_WS EAAAKGGSGSS 12,554 PERV_Q4VFZ2_3mutA_WS PAPGSSEAAAK 12,555 MLVMS_P03355_PLV919 GSSEAAAKPAP 12,556 MLVMS_P03355_PLV919 GGSPAPGSS 12,557 BAEVM_P10272_3mutA GSAGSAAGSGEF 12,558 MLVCB_P08361_3mut GGSPAPGGG 12,559 PERV_Q4VFZ2_3mut GGGGSGGGGSGGGGSGGGGS 12,560 MLVMS_P03355_3mut GSSGSSGSS 12,561 PERV_Q4VFZ2_3mutA_WS EAAAKEAAAKEAAAKEAAAKEAAAKEAAAK 12,562 PERV_Q4VFZ2_3mut GGGGSEAAAKGGGGS 12,563 MLVCB_P08361_3mutA GGSEAAAKGSS 12,564 MLVAV_P03356_3mutA EAAAKGGGGSEAAAK 12,565 MLVCB_P08361_3mut EAAAKEAAAKEAAAKEAAAKEAAAKEAAAK 12,566 XMRV6_A1Z651_3mutA PAPGGGEAAAK 12,567 MLVMS_P03355_3mutA_WS GSSGGGEAAAK 12,568 PERV_Q4VFZ2_3mutA_WS GSSGSS 12,569 MLVCB_P08361_3mut PAPAPAPAPAPAP 12,570 PERV_Q4VFZ2_3mut GGSPAPGGG 12,571 MLVFF_P26809_3mutA GGSGGSGGSGGSGGS 12,572 MLVCB_P08361_3mutA EAAAKEAAAK 12,573 MLVFF_P26809_3mutA AEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKEAAAKA 12,574 GALV_P21414_3mut PAPAPAPAPAPAP 12,575 WMSV_P03359_3mutA GGGEAAAKGGS 12,576 KORV_Q9TTC1_3mutA EAAAKGGGPAP 12,577 KORV_Q9TTC1_3mut PAPEAAAKGSS 12,578 MLVBM_Q7SVK7_3mutA_WS PAPEAAAKGSS 12,579 FLV_P10273_3mutA PAPGGSEAAAK 12,580 MLVMS_P03355_3mut GSSPAPGGG 12,581 BAEVM_P10272_3mutA GGGEAAAKPAP 12,582 KORV_Q9TTC1-Pro_3mutA GGGGSGGGGS 12,583 MLVMS_P03355_PLV919 GGGEAAAKGSS 12,584 MLVFF_P26809_3mutA PAPGGGGSS 12,585 MLVBM_Q7SVK7_3mutA_WS GSSEAAAK 12,586 BAEVM_P10272_3mutA GGGGGGGG 12,587 MLVMS_P03355_PLV919 PAPGSSGGS 12,588 MLVAV_P03356_3mutA GGGGSGGGGSGGGGSGGGGS 12,589 BAEVM_P10272_3mutA PAP MLVMS_P03355_3mut EAAAKGSSPAP 12,591 XMRV6_A1Z651_3mutA PAPEAAAKGGS 12,592 MLVFF_P26809_3mutA GSSGGGEAAAK 12,593 BAEVM_P10272_3mutA PAPAPAP 12,594 MLVMS_P03355_3mutA_WS GGSEAAAKGGG 12,595 MLVMS_P03355_PLV919 GSSEAAAK 12,596 PERV_Q4VFZ2_3mut GGGG 12,597 MLVMS_P03355_3mutA_WS GGGGGS 12,598 MLVMS_P03355_3mut GGGGSSEAAAK 12,599 PERV_Q4VFZ2_3mut EAAAKEAAAKEAAAKEAAAKEAAAKEAAAK 12,600 SFV3L_P27401-Pro_2mutA GGSEAAAKGSS 12,601 MLVMS_P03355_3mutA_WS PAPGSSGGS 12,602 XMRV6_A1Z651_3mutA GGSPAP 12,603 MLVMS_P03355_3mutA_WS GGGGSSEAAAK 12,604 BAEVM_P10272_3mut GGSGGSGGSGGS 12,605 AVIRE_P03360_3mutA PAPGSSGGS 12,606 MLVFF_P26809_3mutA GSSPAPGGG 12,607 MLVMS_P03355_3mutA_WS GGGGGGG 12,608 MLVMS_P03355_3mutA_WS EAAAKGGGGGS 12,609 MLVMS_P03355_3mutA_WS EAAAKGGSGGG 12,610 MLVMS_P03355_PLV919 GGGGSSEAAAK 12,611 XMRV6_A1Z651_3mutA GGGGSEAAAKGGGGS 12,612 MLVBM_Q7SVK7_3mutA_WS GSSGSS 12,613 MLVMS_P03355_PLV919 GGSGGG 12,614 MLVMS_P03355_PLV919 PAPEAAAKGGG 12,615 AVIRE_P03360_3mutA AEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKEAAAKA 12,616 FOAMV_P14350-Pro_2mutA GGGGGSGSS 12,617 PERV_Q4VFZ2_3mut GSSGSSGSSGSSGSS 12,618 KORV_Q9TTC1-Pro_3mut GGGGSEAAAKGGGGS 12,619 MLVMS_P03355_3mutA_WS GGGGGSPAP 12,620 FLV_P10273_3mut GGGEAAAK 12,621 MLVMS_P03355_3mutA_WS GGSGGSGGSGGS 12,622 FLV_P10273_3mutA GGG MLVMS_P03355_PLV919 GGSPAPEAAAK 12,624 BAEVM_P10272_3mutA EAAAKEAAAK 12,625 FLV_P10273_3mutA GGGEAAAKPAP 12,626 BAEVM_P10272_3mutA GGGEAAAKGGS 12,627 PERV_Q4VFZ2_3mut GGSGGSGGS 12,628 PERV_Q4VFZ2_3mut EAAAKGGGPAP 12,629 XMRV6_A1Z651_3mutA EAAAK 12,630 MLVBM_Q7SVK7_3mutA_WS PAPEAAAKGGG 12,631 PERV_Q4VFZ2_3mut EAAAKGSS 12,632 MLVCB_P08361_3mutA GGSEAAAKGGG 12,633 MLVBM_Q7SVK7_3mutA_WS GGGGSGGGGSGGGGSGGGGS 12,634 XMRV6_A1Z651_3mutA GGGGSGGGGSGGGGSGGGGSGGGGS 12,635 BAEVM_P10272_3mut GGGGSSPAP 12,636 PERV_Q4VFZ2_3mutA_WS GGSGGSGGSGGSGGSGGS 12,637 PERV_Q4VFZ2_3mut GGGEAAAKPAP 12,638 PERV_Q4VFZ2_3mut EAAAKEAAAK 12,639 BAEVM_P10272_3mutA GGSGSSEAAAK 12,640 XMRV6_A1Z651_3mutA PAPEAAAKGSS 12,641 WMSV_P03359_3mutA PAPAPAPAPAP 12,642 XMRV6_A1Z651_3mutA GSSGGGEAAAK 12,643 MLVMS_P03355_PLV919 GSSPAPGGG 12,644 MLVFF_P26809_3mutA GGSPAPEAAAK 12,645 MLVFF_P26809_3mut PAPGGSEAAAK 12,646 PERV_Q4VFZ2_3mut GGGGSS 12,647 MLVFF_P26809_3mutA GGSGSSGGG 12,648 BAEVM_P10272_3mutA GSSGGGEAAAK 12,649 MLVMS_P03355_3mutA_WS EAAAKGGS 12,650 MLVBM_Q7SVK7_3mutA_WS GGGPAPGGS 12,651 MLVMS_P03355_PLV919 EAAAKEAAAK 12,652 MLVMS_P03355_PLV919 GSSGSSGSS 12,653 MLVMS_P03355_PLV919 GGGEAAAKPAP 12,654 MLVAV_P03356_3mutA SGSETPGTSESATPES 12,655 FLV_P10273_3mutA PAPAPAPAPAP 12,656 KORV_Q9TTC1-Pro_3mut AEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKEAAAKA 12,657 BAEVM_P10272_3mutA PAPGSSGGG 12,658 MLVMS_P03355_3mutA_WS GSSGGGEAAAK 12,659 XMRV6_A1Z651_3mutA GGGGSGGGGSGGGGSGGGGSGGGGS 12,660 XMRV6_A1Z651_3mutA GGGGSSPAP 12,661 MLVFF_P26809_3mutA GGSGGGPAP 12,662 PERV_Q4VFZ2_3mutA_WS GSS PERV_Q4VFZ2_3mut EAAAKGSSPAP 12,664 MLVMS_P03355_3mut EAAAKGGG 12,665 XMRV6_A1Z651_3mutA GSSGSSGSSGSS 12,666 WMSV_P03359_3mutA PAPEAAAKGSS 12,667 MLVMS_P03355_PLV919 GSSEAAAK 12,668 AVIRE_P03360_3mutA EAAAKGGSGSS 12,669 AVIRE_P03360_3mutA GSSEAAAK 12,670 MLVMS_P03355_3mut GGSGSSEAAAK 12,671 MLVMS_P03355_PLV919 GGSEAAAKGGG 12,672 MLVFF_P26809_3mutA GGGGSGGGGGGGGSGGGGS 12,673 MLVAV_P03356_3mutA PAPAPAPAPAPAP 12,674 MLVFF_P26809_3mut EAAAKPAPGSS 12,675 KORV_Q9TTC1-Pro_3mut PAPGSSEAAAK 12,676 MLVAV_P03356_3mutA GGGGSSPAP 12,677 WMSV_P03359_3mutA EAAAKGGGGGS 12,678 MLVMS_P03355_3mutA_WS GGGEAAAKGGS 12,679 MLVMS_P03355_3mut GGSGSSGGG 12,680 MLVMS_P03355_3mut GGGPAPGGS 12,681 MLVAV_P03356_3mutA PAPGGGGGS 12,682 MLVMS_P03355_PLV919 GGGPAPGSS 12,683 PERV_Q4VFZ2_3mut GGGGGGG 12,684 MLVFF_P26809_3mutA GGSGGGGSS 12,685 MLVCB_P08361_3mutA GGGGGG 12,686 FLV_P10273_3mutA GGSEAAAKGSS 12,687 PERV_Q4VFZ2_3mut GGSPAPGGG 12,688 BAEVM_P10272_3mutA GGSPAPGSS 12,689 AVIRE_P03360_3mutA GGSGGSGGSGGS 12,690 KORV_Q9TTC1_3mut EAAAKEAAAKEAAAKEAAAKEAAAK 12,691 MLVBM_Q7SVK7_3mut PAPGSSGGS 12,692 XMRV6_A1Z651_3mut EAAAKGGGGSS 12,693 PERV_Q4VFZ2_3mutA_WS GGSGGSGGSGGSGGS 12,694 PERV_Q4VFZ2_3mutA_WS PAPGGSGGG 12,695 MLVMS_P03355_PLV919 PAPGSSGGG 12,696 PERV_Q4VFZ2_3mutA_WS GSSGSS 12,697 BAEVM_P10272_3mutA EAAAKGSS 12,698 MLVFF_P26809_3mutA GGGPAP 12,699 MLVMS_P03355_PLV919 EAAAKGGGGGS 12,700 MLVFF_P26809_3mutA EAAAKGGSPAP 12,701 MLVBM_Q7SVK7_3mutA_WS EAAAKEAAAKEAAAKEAAAKEAAAKEAAAK 12,702 WMSV_P03359_3mutA GSSPAPGGG 12,703 MLVBM_Q7SVK7_3mutA_WS GGGEAAAKGSS 12,704 AVIRE_P03360_3mutA GGGGSSEAAAK 12,705 AVIRE_P03360_3mutA GGGGGGGG 12,706 PERV_Q4VFZ2_3mutA_WS PAPGSSEAAAK 12,707 BAEVM_P10272_3mutA EAAAKGSS 12,708 MLVFF_P26809_3mut GSSEAAAKGGG 12,709 MLVCB_P08361_3mutA GGSEAAAK 12,710 MLVBM_Q7SVK7_3mutA_WS GSSEAAAKGGG 12,711 PERV_Q4VFZ2_3mutA_WS PAPGGSGGG 12,712 WMSV_P03359_3mutA GSSGGSGGG 12,713 MLVCB_P08361_3mutA EAAAKGSSGGG 12,714 FLV_P10273_3mutA GSSEAAAK 12,715 MLVCB_P08361_3mutA GSSGGGEAAAK 12,716 MLVMS_P03355_3mut GGGGSGGGGS 12,717 MLVCB_P08361_3mutA EAAAKGGGGSEAAAK 12,718 MLVBM_Q7SVK7_3mutA_WS EAAAKGGG 12,719 PERV_Q4VFZ2_3mutA_WS EAAAKGGSPAP 12,720 MLVMS_P03355_PLV919 GGGPAPGGS 12,721 AVIRE_P03360_3mutA GSSEAAAK 12,722 MLVBM_Q7SVK7_3mutA_WS GSSGGGEAAAK 12,723 PERV_Q4VFZ2_3mut SGSETPGTSESATPES 12,724 MLVMS_P03355_PLV919 GGSGSSPAP 12,725 MLVMS_P03355_3mut GGGGGG 12,726 MLVBM_Q7SVK7_3mutA_WS GGSPAPGGG 12,727 XMRV6_A1Z651_3mutA GGSGSS 12,728 PERV_Q4VFZ2_3mutA_WS PAP MLVBM_Q7SVK7_3mutA_WS EAAAKPAPGSS 12,730 MLVMS_P03355_PLV919 EAAAKGGG 12,731 MLVMS_P03355_3mut GSSEAAAKPAP 12,732 PERV_Q4VFZ2_3mutA_WS GGGGSS 12,733 MLVMS_P03355_3mutA_WS GGSGSSEAAAK 12,734 PERV_Q4VFZ2_3mut GGGGSS 12,735 BAEVM_P10272_3mutA PAPAP 12,736 MLVFF_P26809_3mut PAPEAAAKGGG 12,737 BAEVM_P10272_3mutA EAAAKGGS 12,738 MLVMS_P03355_PLV919 PAPAPAPAPAPAP 12,739 PERV_Q4VFZ2_3mutA_WS GGGGGSEAAAK 12,740 MLVMS_P03355_3mut PAPGGS 12,741 PERV_Q4VFZ2_3mut GGGGSS 12,742 MLVCB_P08361_3mutA GGGGS 12,743 MLVAV_P03356_3mutA GSSPAPEAAAK 12,744 MLVMS_P03355_PLV919 GGGGSSGGS 12,745 MLVFF_P26809_3mutA PAPEAAAKGSS 12,746 MLVMS_P03355_PLV919 GGSGSSEAAAK 12,747 MLVMS_P03355_3mutA_WS EAAAKGGG 12,748 MLVAV_P03356_3mutA PAPGSSEAAAK 12,749 FLV_P10273_3mutA EAAAKGSSGGG 12,750 MLVCB_P08361_3mutA PAPEAAAK 12,751 KORV_Q9TTC1-Pro_3mutA GGSPAPEAAAK 12,752 KORV_Q9TTC1-Pro_3mut GGSGGSGGSGGSGGSGGS 12,753 MLVAV_P03356_3mutA GSSEAAAKPAP 12,754 MLVBM_Q7SVK7_3mutA_WS AEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKEAAAKA 12,755 KORV_Q9TTC1-Pro_3mutA GSSGGGEAAAK 12,756 XMRV6_A1Z651_3mut PAPGGSGGG 12,757 AVIRE_P03360_3mutA PAPGGSEAAAK 12,758 PERV_Q4VFZ2_3mutA_WS GGGGS 12,759 MLVMS_P03355_3mutA_WS GGGGSGGGGSGGGGS 12,760 MLVBM_Q7SVK7_3mutA_WS PAPAPAPAPAP 12,761 PERV_Q4VFZ2_3mutA_WS EAAAKEAAAKEAAAKEAAAKEAAAK 12,762 MLVMS_P03355_3mut GSSGGSEAAAK 12,763 MLVMS_P03355_3mutA_WS GGSGGSGGSGGS 12,764 WMSV_P03359_3mutA EAAAKGSSGGG 12,765 WMSV_P03359_3mutA EAAAKGGG 12,766 PERV_Q4VFZ2_3mutA_WS SGSETPGTSESATPES 12,767 PERV_Q4VFZ2_3mut PAPGSSGGS 12,768 MLVMS_P03355_3mutA_WS PAPEAAAKGSS 12,769 PERV_Q4VFZ2_3mut PAPEAAAK 12,770 AVIRE_P03360_3mutA GSSEAAAKGGG 12,771 BAEVM_P10272_3mutA GSSPAP 12,772 MLVAV_P03356_3mutA EAAAKEAAAKEAAAKEAAAK 12,773 MLVFF_P26809_3mut PAPGGSGSS 12,774 MLVAV_P03356_3mutA GGGGSGGGGSGGGGS 12,775 PERV_Q4VFZ2_3mutA_WS GSSGGSEAAAK 12,776 MLVCB_P08361_3mutA EAAAKGGS 12,777 KORV_Q9TTC1-Pro_3mutA EAAAKGGS 12,778 MLVFF_P26809_3mutA GGSPAP 12,779 MLVMS_P03355_PLV919 GGSGSS 12,780 MLVMS_P03355_PLV919 SGSETPGTSESATPES 12,781 WMSV_P03359_3mut GGGGGGG 12,782 WMSV_P03359_3mut GGSPAPGSS 12,783 MLVCB_P08361_3mutA GGGGSSGGS 12,784 WMSV_P03359_3mut PAPGGS 12,785 MLVMS_P03355_PLV919 PAPGSSGGS 12,786 MLVCB_P08361_3mutA EAAAKEAAAKEAAAKEAAAKEAAAK 12,787 MLVFF_P26809_3mut SGGSSGGSSGSETPGTSESATPESSGGSSGGSS 12,788 PERV_Q4VFZ2_3mut GGSGGSGGSGGSGGS 12,789 BAEVM_P10272_3mutA GSSEAAAK 12,790 PERV_Q4VFZ2_3mut EAAAKEAAAKEAAAKEAAAK 12,791 KORV_Q9TTC1-Pro_3mutA GGSGGSGGSGGSGGS 12,792 MLVMS_P03355_3mut PAPAPAPAPAPAP 12,793 MLVMS_P03355_3mut GGSPAPEAAAK 12,794 MLVMS_P03355_PLV919 EAAAK 12,795 WMSV_P03359_3mutA EAAAKGSSGGS 12,796 MLVBM_Q7SVK7_3mutA_WS GGSGGGGSS 12,797 MLVMS_P03355_3mutA_WS GGGEAAAKPAP 12,798 MLVMS_P03355_3mut EAAAKGGSGGG 12,799 XMRV6_A1Z651_3mutA GGGGGSEAAAK 12,800 KORV_Q9TTC1-Pro_3mutA GGGGGG 12,801 BAEVM_P10272_3mutA GGGGGG 12,802 MLVMS_P03355_3mut GGGGGGG 12,803 MLVBM_Q7SVK7_3mutA_WS AEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKEAAAKA 12,804 AVIRE_P03360 PAPGSSGGS 12,805 PERV_Q4VFZ2_3mut GGGGGS 12,806 XMRV6_A1Z651_3mut EAAAKPAP 12,807 XMRV6_A1Z651_3mutA GGG MLVMS_P03355_3mutA_WS AEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKEAAAKA 12,809 FLV_P10273_3mut EAAAKGSSPAP 12,810 MLVMS_P03355_3mut SGSETPGTSESATPES 12,811 BAEVM_P10272_3mutA GGSPAPEAAAK 12,812 MLVMS_P03355_3mut GSSGSSGSSGSS 12,813 MLVAV_P03356_3mutA AEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKEAAAKA 12,814 MLVMS_P03355_3mut GGSPAP 12,815 MLVCB_P08361_3mutA GGGGGSEAAAK 12,816 MLVMS_P03355_3mutA_WS GGGGG 12,817 MLVFF_P26809_3mutA GSSEAAAK 12,818 MLVAV_P03356_3mutA GGS BAEVM_P10272_3mut EAAAKGGSPAP 12,820 MLVCB_P08361_3mutA PAPAPAPAP 12,821 FLV_P10273_3mutA PAPGGGEAAAK 12,822 MLVCB_P08361_3mutA GGGGSSEAAAK 12,823 MLVMS_P03355_3mutA_WS GGGGG 12,824 PERV_Q4VFZ2_3mutA_WS GGSGGSGGSGGSGGSGGS 12,825 PERV_Q4VFZ2_3mut GGGGG 12,826 MLVMS_P03355_3mut PAPEAAAKGGG 12,827 MLVBM_Q7SVK7_3mutA_WS GSSGGGPAP 12,828 XMRV6_A1Z651_3mutA GSSGSSGSSGSSGSSGSS 12,829 PERV_Q4VFZ2_3mutA_WS EAAAKGGSPAP 12,830 PERV_Q4VFZ2_3mut GSSGGSEAAAK 12,831 MLVMS_P03355_PLV919 GSS PERV_Q4VFZ2_3mut EAAAKGGS 12,833 WMSV_P03359_3mutA GGGGGSPAP 12,834 PERV_Q4VFZ2_3mutA_WS EAAAKGSS 12,835 MLVMS_P03355_PLV919 EAAAKGGGGSS 12,836 KORV_Q9TTC1-Pro_3mutA PAPGSSGGG 12,837 PERV_Q4VFZ2_3mut GGGGSSEAAAK 12,838 MLVFF_P26809_3mut PAPAPAP 12,839 MLVMS_P03355_3mut GSSGGSEAAAK 12,840 XMRV6_A1Z651_3mut PAPEAAAKGSS 12,841 MLVMS_P03355_3mutA_WS GGSGGSGGSGGSGGS 12,842 MLVMS_P03355_3mutA_WS GGSGSSPAP 12,843 XMRV6_A1Z651_3mutA GGGGSSPAP 12,844 MLVMS_P03355_PLV919 GGGGS 12,845 MLVCB_P08361_3mutA EAAAKEAAAKEAAAKEAAAK 12,846 PERV_Q4VFZ2_3mutA_WS EAAAKEAAAK 12,847 KORV_Q9TTC1_3mutA PAPGGGEAAAK 12,848 BAEVM_P10272_3mutA GSSGGSEAAAK 12,849 XMRV6_A1Z651_3mutA EAAAKEAAAKEAAAKEAAAKEAAAKEAAAK 12,850 FLV_P10273_3mut GSSEAAAKPAP 12,851 MLVMS_P03355_3mutA_WS EAAAKPAPGSS 12,852 PERV_Q4VFZ2_3mutA_WS GSSGGSPAP 12,853 XMRV6_A1Z651_3mutA GSSEAAAKGGG 12,854 PERV_Q4VFZ2_3mut GGGEAAAKGGS 12,855 WMSV_P03359_3mutA GSSEAAAKGGG 12,856 MLVFF_P26809_3mut PAPAPAP 12,857 KORV_Q9TTC1-Pro_3mutA EAAAKGGSPAP 12,858 MLVMS_P03355_3mutA_WS PAPGGSEAAAK 12,859 PERV_Q4VFZ2_3mut GGGGS 12,860 MLVBM_Q7SVK7_3mutA_WS EAAAKGSSGGG 12,861 KORV_Q9TTC1_3mut EAAAKGGGPAP 12,862 MLVCB_P08361_3mutA EAAAKGSS 12,863 BAEVM_P10272_3mutA GGSPAPGGG 12,864 MLVBM_Q7SVK7_3mutA_WS GGGGSEAAAKGGGGS 12,865 MLVMS_P03355_3mutA_WS GGGEAAAKGGS 12,866 PERV_Q4VFZ2_3mutA_WS EAAAKGGGGSS 12,867 MLVMS_P03355_3mutA_WS EAAAKGGGPAP 12,868 MLVFF_P26809_3mut GSSPAP 12,869 PERV_Q4VFZ2_3mutA_WS EAAAKGGS 12,870 MLVMS_P03355_3mut GGGGSS 12,871 KORV_Q9TTC1-Pro_3mutA EAAAKGSSPAP 12,872 MLVMS_P03355_3mutA_WS GGGPAP 12,873 PERV_Q4VFZ2_3mut EAAAKGSSGGS 12,874 XMRV6_A1Z651_3mutA PAPGGG 12,875 MLVAV_P03356_3mutA GSSPAPEAAAK 12,876 BAEVM_P10272_3mutA GGGPAP 12,877 MLVBM_Q7SVK7_3mutA_WS GSSGGGGGS 12,878 AVIRE_P03360_3mutA SGSETPGTSESATPES 12,879 MLVMS_P03355_PLV919 GGGPAP 12,880 MLVFF_P26809_3mut EAAAKGGGGSS 12,881 XMRV6_A1Z651_3mutA GGGGSSPAP 12,882 XMRV6_A1Z651_3mut GGGGSEAAAKGGGGS 12,883 MLVMS_P03355_3mut GSSPAP 12,884 MLVBM_Q7SVK7_3mutA_WS GGSGSSEAAAK 12,885 FLV_P10273_3mutA SGSETPGTSESATPES 12,886 MLVBM_Q7SVK7_3mutA_WS PAPGGG 12,887 AVIRE_P03360_3mutA GGGEAAAKPAP 12,888 MLVMS_P03355_3mutA_WS EAAAKGGSGSS 12,889 PERV_Q4VFZ2_3mut GGSPAPGGG 12,890 MLVAV_P03356_3mutA PAPGGSGSS 12,891 BAEVM_P10272_3mutA GSSGGSPAP 12,892 MLVFF_P26809_3mutA EAAAKGSSGGG 12,893 PERV_Q4VFZ2_3mut GGGGSGGGGS 12,894 PERV_Q4VFZ2_3mutA_WS GSSGGGGGS 12,895 BAEVM_P10272_3mutA GGGGSSGGS 12,896 MLVBM_Q7SVK7_3mutA_WS EAAAKGGS 12,897 PERV_Q4VFZ2_3mutA_WS GSSGSSGSSGSS 12,898 MLVMS_P03355_3mut GGS MLVMS_P03355_3mutA_WS GSSGGSEAAAK 12,900 MLVBM_Q7SVK7_3mutA_WS SGGSSGGSSGSETPGTSESATPESSGGSSGGSS 12,901 XMRV6_A1Z651 GGGGG 12,902 FLV_P10273_3mutA PAPEAAAKGSS 12,903 PERV_Q4VFZ2_3mut GGGGGG 12,904 WMSV_P03359_3mut EAAAKGGG 12,905 BAEVM_P10272_3mutA GGGGSS 12,906 MLVMS_P03355_3mutA_WS GSSGGGEAAAK 12,907 KORV_Q9TTC1_3mut GGSGSS 12,908 AVIRE_P03360_3mutA EAAAKPAP 12,909 MLVMS_P03355_3mut EAAAKEAAAKEAAAK 12,910 FLV_P10273_3mutA GGGG 12,911 XMRV6_A1Z651_3mutA GSSPAPGGS 12,912 BAEVM_P10272_3mutA GSSGGGGGS 12,913 MLVFF_P26809_3mutA GGGGSSGGS 12,914 MLVAV_P03356_3mutA GGS PERV_Q4VFZ2_3mut GGGGG 12,916 WMSV_P03359_3mutA GSSGSSGSSGSSGSSGSS 12,917 FLV_P10273_3mutA PAPGGGGSS 12,918 MLVAV_P03356_3mutA GGGGGGGG 12,919 BAEVM_P10272_3mutA SGSETPGTSESATPES 12,920 MLVCB_P08361_3mutA PAPGGG 12,921 BAEVM_P10272_3mutA GSSGSSGSS 12,922 MLVCB_P08361_3mutA GGSGSS 12,923 MLVMS_P03355_3mutA_WS EAAAKGGGGSEAAAK 12,924 WMSV_P03359_3mutA GGGGGGGG 12,925 FLV_P10273_3mutA GSSGSS 12,926 MLVMS_P03355_3mutA_WS PAPEAAAKGGS 12,927 XMRV6_A1Z651_3mutA EAAAKEAAAK 12,928 MLVMS_P03355_3mut GGGGSGGGGSGGGGS 12,929 BAEVM_P10272_3mutA EAAAKGSSPAP 12,930 MLVMS_P03355_PLV919 GGGGSSEAAAK 12,931 MLVMS_P03355_3mut GGGGSSEAAAK 12,932 BAEVM_P10272_3mutA PAPGGSGSS 12,933 PERV_Q4VFZ2_3mut GGSGGGEAAAK 12,934 MLVFF_P26809_3mut PAPEAAAKGGS 12,935 PERV_Q4VFZ2_3mut GGGPAPGSS 12,936 AVIRE_P03360_3mut PAPGGSGGG 12,937 PERV_Q4VFZ2_3mutA_WS GGGGGGGG 12,938 PERV_Q4VFZ2_3mutA_WS GSSEAAAK 12,939 MLVMS_P03355_3mutA_WS GGGGSGGGGSGGGGS 12,940 PERV_Q4VFZ2_3mutA_WS EAAAKGGS 12,941 MLVMS_P03355_3mut GGGGGSGSS 12,942 MLVCB_P08361_3mut GGGPAP 12,943 KORV_Q9TTC1-Pro_3mutA EAAAKPAPGGG 12,944 MLVCB_P08361_3mut GSSGGSPAP 12,945 MLVCB_P08361_3mutA SGGSSGGSSGSETPGTSESATPESSGGSSGGSS 12,946 MLVMS_P03355_3mut PAPAPAPAP 12,947 MLVMS_P03355_3mut GSSGGS 12,948 XMRV6_A1Z651_3mutA GSSEAAAKGGG 12,949 MLVMS_P03355_3mut GGSGSSPAP 12,950 MLVMS_P03355_3mutA_WS GSSEAAAKGGS 12,951 MLVMS_P03355_PLV919 EAAAKEAAAKEAAAKEAAAKEAAAK 12,952 BAEVM_P10272_3mut PAPGGGGSS 12,953 KORV_Q9TTC1_3mutA EAAAKGSS 12,954 MLVMS_P03355_3mutA_WS AEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKEAAAKA 12,955 FFV_093209_2mut GGSGGSGGSGGSGGSGGS 12,956 BAEVM_P10272_3mutA GGGGGG 12,957 MLVMS_P03355_PLV919 PAPEAAAK 12,958 BAEVM_P10272_3mutA GGSGSSEAAAK 12,959 MLVAV_P03356_3mutA GGG MLVCB_P08361_3mutA GGGGG 12,961 MLVCB_P08361_3mutA GGSGGSGGSGGS 12,962 KORV_Q9TTC1-Pro_3mutA GSSGSSGSSGSSGSSGSS 12,963 XMRV6_A1Z651_3mutA GSSEAAAKPAP 12,964 FLV_P10273_3mutA GGGEAAAKPAP 12,965 MLVCB_P08361_3mutA GSSGSSGSS 12,966 MLVMS_P03355_3mutA_WS PAPAPAPAP 12,967 MLVMS_P03355_PLV919 EAAAKGGG 12,968 MLVMS_P03355_PLV919 PAPAPAPAPAPAP 12,969 FLV_P10273_3mutA EAAAKGGSGSS 12,970 MLVMS_P03355_3mut GGGGGG 12,971 PERV_Q4VFZ2_3mutA_WS PAPGGG 12,972 MLVCB_P08361_3mutA GGGGGSGSS 12,973 KORV_Q9TTC1_3mutA GGGGSGGGGSGGGGSGGGGS 12,974 XMRV6_A1Z651_3mut GGSGGSGGS 12,975 KORV_Q9TTC1-Pro_3mutA EAAAKPAPGGG 12,976 MLVMS_P03355_3mutA_WS AEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKEAAAKA 12,977 XMRV6_A1Z651 GGGGSGGGGSGGGGSGGGGSGGGGSGGGGS 12,978 FLV_P10273_3mutA EAAAKGGGGSEAAAK 12,979 PERV_Q4VFZ2_3mutA_WS GGGPAPGSS 12,980 AVIRE_P03360_3mutA GGGGG 12,981 MLVMS_P03355_3mutA_WS GGGGSGGGGSGGGGSGGGGSGGGGSGGGGS 12,982 MLVMS_P03355_3mut GGGGSGGGGS 12,983 MLVMS_P03355_3mutA_WS EAAAKGGSPAP 12,984 XMRV6_A1Z651_3mutA EAAAKGSSPAP 12,985 AVIRE_P03360_3mutA PAPGGSGSS 12,986 KORV_Q9TTC1-Pro_3mutA GSS MLVBM_Q7SVK7_3mutA_WS GSS WMSV_P03359_3mut GGGPAPGSS 12,989 MLVFF_P26809_3mutA EAAAKPAP 12,990 MLVMS_P03355_3mut GSSPAPEAAAK 12,991 FLV_P10273_3mutA GGSPAPGSS 12,992 MLVBM_Q7SVK7_3mutA_WS GGGGGSEAAAK 12,993 XMRV6_A1Z651_3mut PAPEAAAKGGG 12,994 WMSV_P03359_3mutA PAPGGG 12,995 PERV_Q4VFZ2_3mut GGSPAPEAAAK 12,996 WMSV_P03359_3mutA GGSGGGGSS 12,997 PERV_Q4VFZ2_3mut EAAAKGGGGSS 12,998 PERV_Q4VFZ2_3mut EAAAKGGSPAP 12,999 AVIRE_P03360_3mut GGSGGGGSS 13,000 WMSV_P03359_3mutA PAPGSSEAAAK 13,001 MLVFF_P26809_3mut GSSEAAAK 13,002 MLVMS_P03355_PLV919 GSAGSAAGSGEF 13,003 AVIRE_P03360_3mutA EAAAKGGSGSS 13,004 MLVMS_P03355_3mut GGSEAAAKPAP 13,005 MLVMS_P03355_PLV919 GGGGSGGGGSGGGGSGGGGSGGGGS 13,006 MLVFF_P26809_3mutA PAPGSSEAAAK 13,007 PERV_Q4VFZ2_3mutA_WS GGGGSSPAP 13,008 MLVMS_P03355_3mutA_WS PAPAPAP 13,009 MLVCB_P08361_3mutA EAAAKPAPGGG 13,010 MLVBM_Q7SVK7_3mutA_WS GGGPAPGSS 13,011 BAEVM_P10272_3mutA PAP MLVMS_P03355_3mutA_WS PAPGGSGGG 13,013 MLVMS_P03355_3mutA_WS GGSGGSGGSGGSGGS 13,014 MLVBM_Q7SVK7_3mutA_WS PAPAPAPAP 13,015 XMRV6_A1Z651_3mut GSSPAPGGG 13,016 MLVMS_P03355_3mutA_WS GSSPAPGGG 13,017 MLVMS_P03355_3mut PAPGGG 13,018 MLVMS_P03355_PLV919 GGGEAAAKGSS 13,019 WMSV_P03359_3mut EAAAKGSS 13,020 KORV_Q9TTC1-Pro_3mutA EAAAKGGS 13,021 PERV_Q4VFZ2_3mut EAAAKEAAAKEAAAKEAAAKEAAAK 13,022 PERV_Q4VFZ2_3mut PAPEAAAKGGG 13,023 MLVMS_P03355_PLV919 EAAAKGSSGGG 13,024 MLVFF_P26809_3mut AEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKEAAAKA 13,025 PERV_Q4VFZ2 EAAAKEAAAKEAAAKEAAAKEAAAKEAAAK 13,026 MLVAV_P03356_3mutA GSSGGSGGG 13,027 MLVFF_P26809_3mut GSSGSSGSSGSS 13,028 PERV_Q4VFZ2_3mutA_WS GGSPAPGGG 13,029 MLVMS_P03355_PLV919 GSS BAEVM_P10272_3mut GGGPAPGSS 13,031 MLVMS_P03355_3mutA_WS GGGGSS 13,032 KORV_Q9TTC1_3mutA GSSGGSGGG 13,033 BAEVM_P10272_3mutA EAAAKEAAAKEAAAK 13,034 MLVCB_P08361_3mutA SGGSSGGSSGSETPGTSESATPESSGGSSGGSS 13,035 FLV_P10273_3mutA PAPGGGGGS 13,036 PERV_Q4VFZ2_3mut PAPAPAPAPAP 13,037 KORV_Q9TTC1-Pro_3mutA EAAAK 13,038 MLVMS_P03355_3mutA_WS GGG MLVCB_P08361_3mut GGSEAAAKGGG 13,040 BAEVM_P10272_3mutA GGGGGSGSS 13,041 MLVAV_P03356_3mutA EAAAKGSSPAP 13,042 MLVBM_Q7SVK7_3mutA_WS GGSGGSGGS 13,043 XMRV6_A1Z651_3mut EAAAKPAPGGG 13,044 KORV_Q9TTC1-Pro_3mutA GGGPAPEAAAK 13,045 FLV_P10273_3mutA GGSPAPEAAAK 13,046 MLVMS_P03355_3mutA_WS GGSGGSGGSGGSGGS 13,047 MLVFF_P26809_3mut EAAAKGGSGSS 13,048 MLVMS_P03355_PLV919 GGGEAAAKGGS 13,049 MLVBM_Q7SVK7_3mutA_WS PAPAPAPAP 13,050 BAEVM_P10272_3mutA EAAAKEAAAKEAAAKEAAAK 13,051 MLVMS_P03355_3mut EAAAKPAP 13,052 XMRV6_A1Z651_3mut EAAAKEAAAK 13,053 MLVBM_Q7SVK7_3mutA_WS EAAAKGGG 13,054 BAEVM_P10272_3mut EAAAKGSS 13,055 MLVAV_P03356_3mutA EAAAKEAAAKEAAAKEAAAKEAAAKEAAAK 13,056 MLVFF_P26809_3mut GGGPAPGSS 13,057 PERV_Q4VFZ2_3mutA_WS GGGG 13,058 PERV_Q4VFZ2_3mut EAAAKGGSGSS 13,059 MLVMS_P03355_PLV919 GGGGSGGGGSGGGGS 13,060 MLVMS_P03355_3mutA_WS EAAAK 13,061 MLVMS_P03355_3mutA_WS GGGGSS 13,062 PERV_Q4VFZ2 PAPEAAAKGGS 13,063 MLVCB_P08361_3mut GSS MLVMS_P03355_3mut GSAGSAAGSGEF 13,065 MLVFF_P26809_3mutA EAAAKEAAAKEAAAKEAAAKEAAAKEAAAK 13,066 KORV_Q9TTC1-Pro_3mut GGGGGGGGS 13,067 AVIRE_P03360_3mutA EAAAK 13,068 MLVMS_P03355_3mut GGGPAPGGS 13,069 PERV_Q4VFZ2_3mut GGGGSGGGGSGGGGS 13,070 MLVMS_P03355_PLV919 PAPGGG 13,071 MLVMS_P03355_3mutA_WS GGGEAAAKPAP 13,072 PERV_Q4VFZ2_3mutA_WS EAAAKPAPGSS 13,073 KORV_Q9TTC1-Pro_3mutA PAPGSS 13,074 KORV_Q9TTC1_3mutA GSAGSAAGSGEF 13,075 PERV_Q4VFZ2_3mut PAPGGGGSS 13,076 KORV_Q9TTC1-Pro_3mutA GSSGGGEAAAK 13,077 MLVCB_P08361_3mutA GSS AVIRE_P03360_3mutA GSSGSSGSSGSS 13,079 XMRV6_A1Z651_3mutA PAPEAAAKGGG 13,080 MLVMS_P03355_PLV919 GGGPAPEAAAK 13,081 MLVCB_P08361_3mutA PAPGGGGGS 13,082 MLVCB_P08361_3mutA EAAAKEAAAKEAAAKEAAAK 13,083 PERV_Q4VFZ2_3mutA_WS GGGGGSPAP 13,084 MLVFF_P26809_3mutA GSSGSSGSSGSSGSS 13,085 PERV_Q4VFZ2 GSSPAPEAAAK 13,086 MLVMS_P03355_PLV919 GSSGSSGSSGSSGSSGSS 13,087 MLVBM_Q7SVK7_3mutA_WS GSSGSSGSSGSSGSSGSS 13,088 MLVMS_P03355_3mutA_WS GGSPAPEAAAK 13,089 MLVAV_P03356_3mutA GSSGGG 13,090 BAEVM_P10272_3mut EAAAKGSSGGS 13,091 KORV_Q9TTC1-Pro_3mutA GGSGSSEAAAK 13,092 MLVMS_P03355_3mutA_WS GGGPAPEAAAK 13,093 MLVFF_P26809_3mutA GGGPAPGGS 13,094 MLVMS_P03355_3mutA_WS GGGGG 13,095 MLVMS_P03355_PLV919 GGGEAAAKPAP 13,096 MLVBM_Q7SVK7_3mutA_WS GGGGSGGGGS 13,097 WMSV_P03359_3mut GGGPAPEAAAK 13,098 PERV_Q4VFZ2_3mut GGSGSSEAAAK 13,099 MLVMS_P03355_PLV919 EAAAKGGGPAP 13,100 MLVMS_P03355_3mutA_WS GSSGSSGSSGSSGSS 13,101 KORV_Q9TTC1-Pro_3mutA PAPAP 13,102 WMSV_P03359_3mutA GGSPAPGSS 13,103 MLVAV_P03356_3mutA GGSGGGPAP 13,104 MLVMS_P03355_3mut GGSPAP 13,105 MLVMS_P03355_PLV919 EAAAKGGSPAP 13,106 PERV_Q4VFZ2_3mut GSSPAPGGG 13,107 KORV_Q9TTC1-Pro_3mutA GSAGSAAGSGEF 13,108 MLVMS_P03355_3mut GGSPAP 13,109 PERV_Q4VFZ2_3mut GSSGSS 13,110 KORV_Q9TTC1-Pro_3mut GGGPAPGSS 13,111 MLVMS_P03355_3mutA_WS AEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKEAAAKA 13,112 FOAMV_P14350 PAPGSSGGG 13,113 MLVMS_P03355_PLV919 GGSEAAAKPAP 13,114 BAEVM_P10272_3mutA GGGGGS 13,115 MLVCB_P08361_3mutA PAPEAAAKGGS 13,116 MLVMS_P03355_3mutA_WS EAAAKEAAAKEAAAKEAAAKEAAAKEAAAK 13,117 BAEVM_P10272_3mutA GGSEAAAK 13,118 BAEVM_P10272_3mutA GSSPAPEAAAK 13,119 MLVMS_P03355_3mutA_WS PAPGGG 13,120 WMSV_P03359_3mut EAAAKPAP 13,121 PERV_Q4VFZ2_3mut GSSGSSGSSGSSGSS 13,122 WMSV_P03359_3mut PAPGGG 13,123 MLVBM_Q7SVK7_3mutA_WS GGSGGGEAAAK 13,124 BAEVM_P10272_3mutA PAPGGS 13,125 MLVMS_P03355_3mut GGSGGSGGSGGS 13,126 MLVBM_Q7SVK7_3mutA_WS EAAAKEAAAKEAAAKEAAAK 13,127 PERV_Q4VFZ2_3mut GGSEAAAKGGG 13,128 WMSV_P03359_3mutA GGGPAP 13,129 BAEVM_P10272_3mutA GGGGSGGGGSGGGGSGGGGSGGGGSGGGGS 13,130 XMRV6_A1Z651_3mut GGSPAPGSS 13,131 KORV_Q9TTC1_3mut GGGPAPGSS 13,132 MLVMS_P03355_3mut GGGGSSGGS 13,133 BAEVM_P10272_3mutA GGGEAAAKGSS 13,134 KORV_Q9TTC1-Pro_3mutA PAPAP 13,135 MLVBM_Q7SVK7_3mutA_WS GGSPAPGGG 13,136 PERV_Q4VFZ2_3mut PAPGSS 13,137 PERV_Q4VFZ2_3mutA_WS GSSGGSPAP 13,138 MLVBM_Q7SVK7_3mutA_WS EAAAKGGGGSEAAAK 13,139 PERV_Q4VFZ2_3mut GSSEAAAKGGS 13,140 KORV_Q9TTC1-Pro_3mut PAPAPAPAP 13,141 KORV_Q9TTC1-Pro_3mutA GGSEAAAKPAP 13,142 WMSV_P03359_3mutA PAPGGS 13,143 FLV_P10273_3mutA EAAAKGGGPAP 13,144 PERV_Q4VFZ2_3mut GGSGSSGGG 13,145 AVIRE_P03360_3mutA EAAAKGGSGSS 13,146 BAEVM_P10272_3mutA SGGSSGGSSGSETPGTSESATPESSGGSSGGSS 13,147 MLVCB_P08361_3mutA GSSEAAAKGGS 13,148 XMRV6_A1Z651_3mutA GGGGG 13,149 BAEVM_P10272_3mutA GGGGSGGGGSGGGGSGGGGSGGGGSGGGGS 13,150 SFV3L_P27401_2mutA GGGEAAAKGSS 13,151 MLVMS_P03355_PLV919 EAAAKGGGGSEAAAK 13,152 KORV_Q9TTC1_3mutA EAAAKGGG 13,153 AVIRE_P03360_3mut GGSGGG 13,154 MLVMS_P03355_3mutA_WS GGSGSSGGG 13,155 MLVMS_P03355_PLV919 GGGGSGGGGSGGGGSGGGGSGGGGSGGGGS 13,156 KORV_Q9TTC1_3mut GGGGSEAAAKGGGGS 13,157 KORV_Q9TTC1_3mutA PAPAPAPAPAP 13,158 FLV_P10273_3mutA GGS MLVBM_Q7SVK7_3mutA_WS GGGGGSEAAAK 13,160 MLVBM_Q7SVK7_3mutA_WS GSSGSSGSSGSSGSS 13,161 MLVMS_P03355_3mutA_WS EAAAKEAAAKEAAAKEAAAKEAAAK 13,162 MLVMS_P03355_3mut GGSGSSGGG 13,163 PERV_Q4VFZ2_3mut PAP MLVFF_P26809_3mut GSSPAPEAAAK 13,165 MLVAV_P03356_3mutA EAAAKGGGGSS 13,166 MLVMS_P03355_3mut GGGEAAAKGGS 13,167 XMRV6_A1Z651_3mut GGSGGGPAP 13,168 MLVBM_Q7SVK7_3mutA_WS GSAGSAAGSGEF 13,169 BAEVM_P10272_3mutA GSSEAAAK 13,170 MLVCB_P08361_3mut PAPGSS 13,171 MLVMS_P03355_3mut EAAAKEAAAKEAAAK 13,172 MLVAV_P03356_3mutA GSAGSAAGSGEF 13,173 XMRV6_A1Z651_3mutA GSSGSSGSSGSS 13,174 BAEVM_P10272_3mutA AEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKEAAAKA 13,175 KORV_Q9TTC1-Pro_3mut GGGGSSEAAAK 13,176 WMSV_P03359_3mut GSSGGGEAAAK 13,177 MLVBM_Q7SVK7_3mutA_WS EAAAKPAP 13,178 MLVFF_P26809_3mutA GGSPAPGGG 13,179 KORV_Q9TTC1_3mutA PAPEAAAK 13,180 FLV_P10273_3mutA GSSGSSGSS 13,181 MLVBM_Q7SVK7_3mutA_WS GSSGGGEAAAK 13,182 FLV_P10273_3mutA GGSPAP 13,183 MLVBM_Q7SVK7_3mutA_WS GSAGSAAGSGEF 13,184 KORV_Q9TTC1-Pro_3mutA PAPGGSEAAAK 13,185 MLVMS_P03355_PLV919 GGSPAPEAAAK 13,186 MLVBM_Q7SVK7_3mutA_WS GGGGGSPAP 13,187 MLVBM_Q7SVK7_3mutA_WS EAAAKGSSPAP 13,188 WMSV_P03359_3mut EAAAKGGGPAP 13,189 MLVBM_Q7SVK7_3mutA_WS PAPGSS 13,190 KORV_Q9TTC1-Pro_3mutA GGSGSSGGG 13,191 BAEVM_P10272_3mut SGGSSGGSSGSETPGTSESATPESSGGSSGGSS 13,192 FFV_093209-Pro_2mut GGSGGSGGSGGSGGSGGS 13,193 WMSV_P03359_3mutA GGSGGSGGS 13,194 PERV_Q4VFZ2_3mutA_WS GGGGG 13,195 PERV_Q4VFZ2_3mutA_WS GGGPAP 13,196 FLV_P10273_3mutA PAPGGSGGG 13,197 XMRV6_A1Z651_3mutA GGGGSEAAAKGGGGS 13,198 XMRV6_A1Z651_3mut EAAAKGSSGGG 13,199 KORV_Q9TTC1-Pro_3mutA GSSGGSEAAAK 13,200 WMSV_P03359_3mut EAAAKGGSGSS 13,201 PERV_Q4VFZ2_3mut PAPAPAPAPAP 13,202 PERV_Q4VFZ2_3mut GGGGSGGGGSGGGGSGGGGSGGGGSGGGGS 13,203 MLVMS_P03355_3mutA_WS GGGGGGG 13,204 KORV_Q9TTC1_3mutA EAAAK 13,205 KORV_Q9TTC1-Pro_3mutA GGGEAAAKGGS 13,206 KORV_Q9TTC1-Pro_3mutA GGGEAAAKGGS 13,207 PERV_Q4VFZ2_3mutA_WS GGGGGSPAP 13,208 XMRV6_A1Z651_3mut GGGGSGGGGSGGGGSGGGGS 13,209 MLVFF_P26809_3mut GGGGGGG 13,210 MLVFF_P26809_3mut PAPAPAPAPAPAP 13,211 AVIRE_P03360_3mutA GSSPAPGGG 13,212 FLV_P10273_3mutA GGGGGSPAP 13,213 MLVMS_P03355_3mutA_WS GGGGSGGGGSGGGGS 13,214 MLVMS_P03355_3mut GGGGSGGGGSGGGGS 13,215 KORV_Q9TTC1_3mut GSSEAAAKGGS 13,216 MLVAV_P03356_3mutA GSSGSSGSSGSSGSS 13,217 MLVMS_P03355_3mut EAAAKGGGGGS 13,218 PERV_Q4VFZ2_3mutA_WS GSSGGGGGS 13,219 PERV_Q4VFZ2_3mut GGGEAAAKPAP 13,220 MLVMS_P03355_3mut GSSGGSPAP 13,221 PERV_Q4VFZ2_3mutA_WS GSSGGGPAP 13,222 BAEVM_P10272_3mutA GGGGGSGSS 13,223 MLVMS_P03355_PLV919 AEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKEAAAKA 13,224 BAEVM_P10272_3mut PAPEAAAK 13,225 MLVMS_P03355_3mut GGGGSGGGGSGGGGS 13,226 FLV_P10273_3mutA GGSGSSGGG 13,227 WMSV_P03359_3mutA EAAAKGGS 13,228 PERV_Q4VFZ2_3mut EAAAKGSSPAP 13,229 MLVCB_P08361_3mut EAAAKGGSGSS 13,230 WMSV_P03359_3mutA GSSGSS 13,231 PERV_Q4VFZ2_3mutA_WS PAPAPAPAP 13,232 MLVMS_P03355_PLV919 GGSGGG 13,233 PERV_Q4VFZ2_3mutA_WS GSS MLVBM_Q7SVK7_3mutA_WS PAP KORV_Q9TTC1-Pro_3mutA GGSGSSEAAAK 13,236 MLVFF_P26809_3mut PAPEAAAKGSS 13,237 KORV_Q9TTC1-Pro_3mutA GGSGGS 13,238 MLVCB_P08361_3mutA GGGGGGG 13,239 PERV_Q4VFZ2_3mutA_WS GGSPAPEAAAK 13,240 MLVBM_Q7SVK7_3mut EAAAKEAAAKEAAAKEAAAKEAAAKEAAAK 13,241 KORV_Q9TTC1_3mutA GGSPAP 13,242 MLVMS_P03355_3mut GGSEAAAKGGG 13,243 PERV_Q4VFZ2_3mut GGGGSGGGGS 13,244 FLV_P10273_3mutA GGGEAAAK 13,245 BAEVM_P10272_3mutA GGGGSGGGGSGGGGSGGGGSGGGGSGGGGS 13,246 SFV3L_P27401_2mut GGSEAAAKPAP 13,247 KORV_Q9TTC1-Pro_3mutA GSSGGGEAAAK 13,248 MLVMS_P03355_PLV919 GGGGGSEAAAK 13,249 MLVMS_P03355_PLV919 EAAAKGGSGGG 13,250 MLVMS_P03355_3mutA_WS GGGGSSPAP 13,251 MLVAV_P03356_3mutA EAAAKEAAAK 13,252 MLVMS_P03355_3mutA_WS AEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKEAAAKA 13,253 SFV3L_P27401_2mut GSSGSSGSSGSSGSS 13,254 MLVMS_P03355_PLV919 GSSGGG 13,255 KORV_Q9TTC1-Pro_3mutA GSSGGS 13,256 MLVFF_P26809_3mutA GGGGSGGGGS 13,257 XMRV6_A1Z651_3mutA PAPGSS 13,258 MLVBM_Q7SVK7_3mutA_WS GGGPAPEAAAK 13,259 XMRV6_A1Z651_3mutA EAAAKGGS 13,260 MLVFF_P26809_3mut GSS KORV_Q9TTC1_3mutA GGGG 13,262 PERV_Q4VFZ2_3mut GGGGGSEAAAK 13,263 AVIRE_P03360_3mutA GSSGSSGSSGSSGSS 13,264 MLVMS_P03355_PLV919 PAPGGSGGG 13,265 PERV_Q4VFZ2_3mut GGGPAP 13,266 PERV_Q4VFZ2_3mut GGGPAPEAAAK 13,267 AVIRE_P03360_3mutA GGGEAAAK 13,268 MLVCB_P08361_3mut GGG MLVFF_P26809_3mutA EAAAKPAPGSS 13,270 XMRV6_A1Z651_3mutA GGSGSSEAAAK 13,271 PERV_Q4VFZ2_3mutA_WS EAAAKGSS 13,272 MLVMS_P03355_3mut GGSGSSEAAAK 13,273 BAEVM_P10272_3mut GGSGGG 13,274 MLVBM_Q7SVK7_3mutA_WS GGGPAP 13,275 MLVMS_P03355_PLV919 GGSPAPGGG 13,276 PERV_Q4VFZ2_3mutA_WS GGGGGSEAAAK 13,277 MLVFF_P26809_3mutA EAAAKGSSGGS 13,278 MLVBM_Q7SVK7_3mut PAPAP 13,279 XMRV6_A1Z651_3mut GSSPAPGGS 13,280 MLVBM_Q7SVK7_3mutA_WS GSSEAAAKGGG 13,281 WMSV_P03359_3mutA EAAAKGGGGGS 13,282 PERV_Q4VFZ2_3mut GSSGSSGSSGSSGSS 13,283 MLVCB_P08361_3mutA EAAAKGGGGSS 13,284 PERV_Q4VFZ2_3mut EAAAKGSS 13,285 PERV_Q4VFZ2_3mut EAAAKEAAAKEAAAKEAAAKEAAAKEAAAK 13,286 AVIRE_P03360_3mutA EAAAKGGS 13,287 MLVCB_P08361_3mut GSSGGSEAAAK 13,288 MLVAV_P03356_3mutA EAAAKPAPGGS 13,289 PERV_Q4VFZ2_3mut GGSGGS 13,290 MLVAV_P03356_3mutA EAAAKGSSGGG 13,291 AVIRE_P03360_3mutA GGSGGSGGSGGS 13,292 PERV_Q4VFZ2_3mut GGGGGGGG 13,293 KORV_Q9TTC1_3mutA GGSGSSEAAAK 13,294 MLVCB_P08361_3mutA EAAAKGGG 13,295 MLVBM_Q7SVK7_3mutA_WS GGGGSGGGGSGGGGS 13,296 MLVCB_P08361_3mut GGSGGSGGSGGS 13,297 PERV_Q4VFZ2_3mutA_WS PAPAPAPAPAP 13,298 WMSV_P03359_3mut EAAAKEAAAKEAAAKEAAAK 13,299 PERV_Q4VFZ2_3mut GGSGGSGGS 13,300 XMRV6_A1Z651_3mutA PAPGGGGSS 13,301 BAEVM_P10272_3mutA GSSEAAAKGGS 13,302 MLVCB_P08361_3mut GSSGGGPAP 13,303 MLVCB_P08361_3mutA GGSGSS 13,304 MLVBM_Q7SVK7_3mutA_WS GGGGGSEAAAK 13,305 MLVAV_P03356_3mutA GSSEAAAK 13,306 PERV_Q4VFZ2_3mutA_WS GGGGGSGSS 13,307 MLVBM_Q7SVK7_3mutA_WS EAAAKGGSGSS 13,308 MLVFF_P26809_3mut PAP FLV_P10273_3mutA GGGGG 13,310 MLVMS_P03355_3mutA_WS EAAAK 13,311 PERV_Q4VFZ2_3mut GSS FLV_P10273_3mutA PAPAPAPAPAPAP 13,313 KORV_Q9TTC1-Pro_3mutA EAAAKEAAAKEAAAKEAAAK 13,314 MLVCB_P08361_3mut EAAAKGGGGSEAAAK 13,315 XMRV6_A1Z651_3mut PAPGGSGGG 13,316 MLVBM_Q7SVK7_3mutA_WS GGSGGGPAP 13,317 WMSV_P03359_3mutA GGGGSSEAAAK 13,318 MLVBM_Q7SVK7_3mutA_WS PAPGGGGSS 13,319 MLVCB_P08361_3mut GGSGGSGGSGGS 13,320 PERV_Q4VFZ2_3mutA_WS PAPGGSGGG 13,321 MLVMS_P03355_3mutA_WS GSSPAPGGS 13,322 MLVCB_P08361_3mutA GSSGSSGSS 13,323 MLVFF_P26809_3mut PAPGGGGGS 13,324 MLVBM_Q7SVK7_3mutA_WS GSSPAP 13,325 PERV_Q4VFZ2_3mut GGSGGG 13,326 KORV_Q9TTC1-Pro_3mut EAAAKGGGGSEAAAK 13,327 PERV_Q4VFZ2_3mutA_WS GGSPAPEAAAK 13,328 PERV_Q4VFZ2_3mutA_WS EAAAKPAP 13,329 BAEVM_P10272_3mut GGGGSGGGGSGGGGSGGGGSGGGGSGGGGS 13,330 MLVMS_P03355_3mut EAAAKGGGGSS 13,331 MLVFF_P26809_3mut EAAAKEAAAK 13,332 MLVCB_P08361_3mut GSSEAAAKGGS 13,333 PERV_Q4VFZ2_3mut GGSPAP 13,334 KORV_Q9TTC1-Pro_3mutA EAAAKEAAAKEAAAKEAAAK 13,335 MLVMS_P03355_3mutA_WS GSSGSSGSSGSSGSS 13,336 BAEVM_P10272_3mut PAPEAAAK 13,337 MLVMS_P03355_3mut GSSGGSPAP 13,338 PERV_Q4VFZ2 GGGPAPGGS 13,339 BAEVM_P10272_3mutA EAAAKPAPGGS 13,340 MLVMS_P03355_PLV919 GGGGSGGGGS 13,341 PERV_Q4VFZ2 GGGEAAAK 13,342 KORV_Q9TTC1-Pro_3mut EAAAKGGGGGS 13,343 FLV_P10273_3mutA GGSPAPGSS 13,344 MLVMS_P03355_3mut GSSPAPEAAAK 13,345 MLVMS_P03355_3mutA_WS GSAGSAAGSGEF 13,346 MLVBM_Q7SVK7_3mutA_WS EAAAK 13,347 BAEVM_P10272_3mutA EAAAKGGGGSS 13,348 BAEVM_P10272_3mutA GGG WMSV_P03359_3mut GGSGSSPAP 13,350 BAEVM_P10272_3mut GGSEAAAKPAP 13,351 MLVBM_Q7SVK7_3mutA_WS EAAAKGGSGSS 13,352 MLVCB_P08361_3mut PAPGSS 13,353 MLVAV_P03356_3mutA PAPEAAAKGGG 13,354 MLVCB_P08361_3mutA AEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKEAAAKA 13,355 FOAMV_P14350-Pro_2mut GSSGSSGSS 13,356 PERV_Q4VFZ2_3mut PAPGGG 13,357 MLVMS_P03355_3mut PAPGGS 13,358 PERV_Q4VFZ2_3mut GSSGGG 13,359 MLVMS_P03355_PLV919 GSSGSSGSSGSSGSSGSS 13,360 WMSV_P03359_3mut PAP AVIRE_P03360_3mutA EAAAKGSSPAP 13,362 MLVBM_Q7SVK7_3mutA_WS GSSGSSGSSGSS 13,363 MLVMS_P03355_PLV919 GGGGSGGGGSGGGGSGGGGSGGGGS 13,364 AVIRE_P03360 GGGGS 13,365 PERV_Q4VFZ2_3mut EAAAKGSSGGG 13,366 MLVBM_Q7SVK7_3mutA_WS GGGGGG 13,367 KORV_Q9TTC1-Pro_3mut GGSGSSEAAAK 13,368 PERV_Q4VFZ2_3mut GSSPAPEAAAK 13,369 MLVBM_Q7SVK7_3mutA_WS GGGGSGGGGS 13,370 MLVBM_Q7SVK7_3mutA_WS GSSGGGGGS 13,371 MLVAV_P03356_3mutA GSAGSAAGSGEF 13,372 WMSV_P03359_3mutA GGGEAAAKGSS 13,373 BAEVM_P10272_3mutA AEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKEAAAKA 13,374 FFV_093209-Pro_2mut PAPGGSGGG 13,375 MLVCB_P08361_3mutA EAAAKEAAAKEAAAKEAAAKEAAAK 13,376 SFV3L_P27401_2mut GGSGSSPAP 13,377 MLVMS_P03355_PLV919 GGGGGG 13,378 PERV_Q4VFZ2_3mut EAAAKEAAAKEAAAKEAAAKEAAAK 13,379 PERV_Q4VFZ2_3mut EAAAKGSSPAP 13,380 MLVFF_P26809_3mut GGGPAPGGS 13,381 MLVBM_Q7SVK7_3mutA_WS AEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKEAAAKA 13,382 SFV3L_P27401 PAP PERV_Q4VFZ2_3mut EAAAKGGS 13,384 MLVMS_P03355_PLV919 GSSGGSEAAAK 13,385 WMSV_P03359_3mutA GGSGSSEAAAK 13,386 KORV_Q9TTC1-Pro_3mutA EAAAKEAAAKEAAAK 13,387 PERV_Q4VFZ2 GGSGGGEAAAK 13,388 MLVMS_P03355_3mutA_WS GGGGSGGGGSGGGGSGGGGS 13,389 BAEVM_P10272_3mut EAAAKGSS 13,390 XMRV6_A1Z651_3mutA GSSGGGGGS 13,391 WMSV_P03359_3mutA GSSGSSGSSGSSGSSGSS 13,392 MLVFF_P26809_3mutA GGSGSS 13,393 MLVAV_P03356_3mutA EAAAKGGGGSEAAAK 13,394 MLVMS_P03355_PLV919 EAAAKGGGPAP 13,395 PERV_Q4VFZ2 GGSEAAAKGGG 13,396 MLVAV_P03356_3mutA EAAAKEAAAKEAAAKEAAAKEAAAKEAAAK 13,397 MLVBM_Q7SVK7_3mut EAAAKEAAAKEAAAKEAAAKEAAAKEAAAK 13,398 KORV_Q9TTC1-Pro_3mutA GSSPAPEAAAK 13,399 MLVFF_P26809_3mutA GGGGSEAAAKGGGGS 13,400 PERV_Q4VFZ2_3mut GSSGSSGSSGSS 13,401 PERV_Q4VFZ2_3mut GGSEAAAK 13,402 MLVFF_P26809_3mutA GGGGGGGG 13,403 MLVMS_P03355_3mut GSSGGG 13,404 XMRV6_A1Z651_3mutA EAAAKGGS 13,405 BAEVM_P10272_3mutA GGGGS 13,406 BAEVM_P10272_3mutA GGSEAAAKGGG 13,407 KORV_Q9TTC1-Pro_3mutA GGSGSSGGG 13,408 KORV_Q9TTC1_3mutA GGSGSSEAAAK 13,409 WMSV_P03359_3mut EAAAKGGSGSS 13,410 MLVBM_Q7SVK7_3mutA_WS GGS BAEVM_P10272_3mutA GGGPAPGSS 13,412 WMSV_P03359_3mutA GSSGSSGSSGSSGSS 13,413 AVIRE_P03360_3mut GGGEAAAKPAP 13,414 XMRV6_A1Z651_3mut GSSGGG 13,415 MLVFF_P26809_3mutA GGSPAPGSS 13,416 PERV_Q4VFZ2_3mut PAPGGS 13,417 MLVCB_P08361_3mut PAPAPAPAPAP 13,418 KORV_Q9TTC1_3mutA GSSGGS 13,419 MLVCB_P08361_3mutA GSSGGSEAAAK 13,420 PERV_Q4VFZ2_3mut EAAAKGSSGGS 13,421 MLVMS_P03355_PLV919 EAAAKGGG 13,422 WMSV_P03359_3mut PAPGGGGGS 13,423 BAEVM_P10272_3mutA GGGGSEAAAKGGGGS 13,424 WMSV_P03359_3mutA EAAAKEAAAKEAAAKEAAAKEAAAKEAAAK 13,425 MLVMS_P03355_3mutA_WS GGS KORV_Q9TTC1-Pro_3mutA GSSGGSPAP 13,427 BAEVM_P10272_3mutA GGG MLVMS_P03355_PLV919 PAPGSS 13,429 KORV_Q9TTC1-Pro_3mut GGSEAAAKGGG 13,430 FLV_P10273_3mutA GGSEAAAKPAP 13,431 PERV_Q4VFZ2_3mutA_WS GGGGSSPAP 13,432 XMRV6_A1Z651_3mutA EAAAKEAAAKEAAAKEAAAKEAAAK 13,433 PERV_Q4VFZ2_3mutA_WS GGGG 13,434 PERV_Q4VFZ2_3mutA_WS GGSEAAAKPAP 13,435 MLVMS_P03355_3mut PAPGSSGGG 13,436 MLVMS_P03355_3mutA_WS PAPEAAAKGGS 13,437 AVIRE_P03360_3mut GGGGSSPAP 13,438 MLVMS_P03355_3mutA_WS GGGGSGGGGSGGGGSGGGGS 13,439 PERV_Q4VFZ2_3mut GGGEAAAK 13,440 MLVMS_P03355_3mut GGGGSS 13,441 MLVFF_P26809_3mut GGSPAPGSS 13,442 XMRV6_A1Z651_3mut GGGGS 13,443 KORV_Q9TTC1-Pro_3mutA EAAAKGSSGGS 13,444 FLV_P10273_3mutA GSS MLVMS_P03355_PLV919 GGGG 13,446 MLVMS_P03355_PLV919 GSSGGS 13,447 MLVMS_P03355_PLV919 GGSGGSGGSGGS 13,448 MLVMS_P03355_3mut PAPEAAAKGGS 13,449 MLVMS_P03355_3mut EAAAKGSSGGG 13,450 BAEVM_P10272_3mutA GSSEAAAK 13,451 KORV_Q9TTC1-Pro_3mutA GSAGSAAGSGEF 13,452 KORV_Q9TTC1_3mutA GGGGGSEAAAK 13,453 MLVCB_P08361_3mut GGGG 13,454 WMSV_P03359_3mut GGGGSSEAAAK 13,455 MLVMS_P03355_PLV919 PAPGGG 13,456 WMSV_P03359_3mutA EAAAKGGSGGG 13,457 MLVAV_P03356_3mutA GGGPAPGGS 13,458 MLVMS_P03355_3mut EAAAKPAP 13,459 PERV_Q4VFZ2_3mutA_WS GSSGSSGSS 13,460 KORV_Q9TTC1-Pro_3mutA GSSPAPGGS 13,461 XMRV6_A1Z651_3mut GGGGGSPAP 13,462 BAEVM_P10272_3mutA GGSGSSGGG 13,463 PERV_Q4VFZ2_3mutA_WS GGGEAAAKGSS 13,464 AVIRE_P03360_3mut GSSEAAAK 13,465 FLV_P10273_3mutA EAAAK 13,466 MLVMS_P03355_3mut EAAAKGGSGSS 13,467 WMSV_P03359_3mut GSSEAAAKGGG 13,468 PERV_Q4VFZ2_3mut PAPGSSGGG 13,469 BAEVM_P10272_3mutA EAAAKGGGGGS 13,470 MLVMS_P03355_3mut GGSEAAAKPAP 13,471 AVIRE_P03360_3mut GGGPAPGGS 13,472 XMRV6_A1Z651_3mut GGGGS 13,473 KORV_Q9TTC1_3mutA GGSGGSGGSGGSGGS 13,474 XMRV6_A1Z651_3mut GGGPAP 13,475 KORV_Q9TTC1-Pro_3mut EAAAKPAP 13,476 MLVBM_Q7SVK7_3mutA_WS GGSEAAAK 13,477 MLVMS_P03355_PLV919 GSSEAAAKPAP 13,478 KORV_Q9TTC1-Pro_3mutA GGSGSS 13,479 MLVMS_P03355_3mut EAAAKPAPGGG 13,480 PERV_Q4VFZ2_3mut GGSPAPEAAAK 13,481 KORV_Q9TTC1_3mutA GGSEAAAKGGG 13,482 AVIRE_P03360_3mutA GGGGSEAAAKGGGGS 13,483 MLVMS_P03355_PLV919 GSSGGGEAAAK 13,484 KORV_Q9TTC1-Pro_3mutA EAAAKGGGPAP 13,485 WMSV_P03359_3mut GSSPAP 13,486 XMRV6_A1Z651_3mutA AEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKEAAAKA 13,487 SFV3L_P27401-Pro GGSEAAAKGSS 13,488 MLVMS_P03355_PLV919 GSSGGSEAAAK 13,489 KORV_Q9TTC1-Pro_3mutA GGSEAAAKGSS 13,490 KORV_Q9TTC1-Pro_3mutA EAAAKGGG 13,491 AVIRE_P03360_3mutA GSSGGSEAAAK 13,492 BAEVM_P10272_3mutA GGGGSEAAAKGGGGS 13,493 KORV_Q9TTC1-Pro_3mut PAPGSSEAAAK 13,494 MLVMS_P03355_3mut PAPEAAAK 13,495 WMSV_P03359_3mut PAPGGSGSS 13,496 PERV_Q4VFZ2_3mutA_WS PAPGSS 13,497 BAEVM_P10272_3mut PAPGGGGGS 13,498 MLVMS_P03355_3mut EAAAKPAPGSS 13,499 MLVBM_Q7SVK7_3mutA_WS GSSPAPGGS 13,500 MLVMS_P03355_PLV919 GGSGSSEAAAK 13,501 MLVMS_P03355_3mut GGGGGG 13,502 KORV_Q9TTC1-Pro_3mutA EAAAKEAAAKEAAAKEAAAK 13,503 MLVBM_Q7SVK7_3mut GGSPAPGSS 13,504 MLVMS_P03355_PLV919 PAPAPAPAPAP 13,505 MLVCB_P08361_3mut GGSGSSPAP 13,506 WMSV_P03359_3mutA EAAAKGGSGGG 13,507 PERV_Q4VFZ2_3mutA_WS GSSGSSGSSGSSGSS 13,508 PERV_Q4VFZ2_3mut AEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKEAAAKA 13,509 KORV_Q9TTC1_3mutA GSSGGGEAAAK 13,510 WMSV_P03359_3mutA GSSGGSEAAAK 13,511 FLV_P10273_3mutA GGGGGGGG 13,512 PERV_Q4VFZ2_3mut PAPGGSEAAAK 13,513 FLV_P10273_3mutA GGGGSSPAP 13,514 BAEVM_P10272_3mutA PAPAPAPAP 13,515 WMSV_P03359_3mut GGSEAAAKPAP 13,516 PERV_Q4VFZ2_3mut PAPGGSGGG 13,517 BAEVM_P10272_3mutA EAAAKEAAAKEAAAKEAAAKEAAAKEAAAK 13,518 MLVMS_P03355_3mut GGGGGGGGSGGGGS 13,519 PERV_Q4VFZ2_3mut GGSGGGPAP 13,520 PERV_Q4VFZ2_3mut GGGPAPEAAAK 13,521 MLVFF_P26809_3mut GGGGGSGSS 13,522 MLVMS_P03355_3mutA_WS GSS MLVCB_P08361_3mut GGGGGSPAP 13,524 MLVMS_P03355_PLV919 GGSPAP 13,525 MLVAV_P03356_3mutA GGGPAPGGS 13,526 KORV_Q9TTC1-Pro_3mutA PAPGSSGGG 13,527 FLV_P10273_3mutA PAPGSSGGG 13,528 WMSV_P03359_3mutA PAPGGS 13,529 MLVBM_Q7SVK7_3mutA_WS GGGEAAAKGSS 13,530 PERV_Q4VFZ2_3mutA_WS GGSEAAAKGSS 13,531 MLVBM_Q7SVK7_3mutA_WS PAPGGSEAAAK 13,532 MLVCB_P08361_3mut GGSEAAAKGGG 13,533 XMRV6_A1Z651_3mutA GGSGGGGSS 13,534 WMSV_P03359_3mut GGGEAAAKPAP 13,535 KORV_Q9TTC1_3mutA EAAAKGSS 13,536 KORV_Q9TTC1-Pro_3mut PAPEAAAKGSS 13,537 MLVFF_P26809_3mut GSAGSAAGSGEF 13,538 PERV_Q4VFZ2_3mut EAAAKGGGGGS 13,539 WMSV_P03359_3mut EAAAKGSSPAP 13,540 WMSV_P03359_3mutA GGGGSEAAAKGGGGS 13,541 XMRV6_A1Z651_3mutA GSSEAAAKPAP 13,542 SFV3L_P27401-Pro_2mutA GGGGGG 13,543 PERV_Q4VFZ2_3mutA_WS PAPGGS 13,544 BAEVM_P10272_3mut PAP AVIRE_P03360_3mut PAPAPAP 13,546 MLVBM_Q7SVK7_3mutA_WS GGGG 13,547 PERV_Q4VFZ2_3mutA_WS GSSGGSEAAAK 13,548 MLVBM_Q7SVK7_3mut GGSGGGGSS 13,549 MLVFF_P26809_3mut GGGGSSGGS 13,550 AVIRE_P03360_3mutA GSSPAPGGG 13,551 PERV_Q4VFZ2_3mutA_WS GGSEAAAKPAP 13,552 MLVMS_P03355_PLV919 PAP KORV_Q9TTC1-Pro_3mut GSSGGS 13,554 PERV_Q4VFZ2_3mut GGGGG 13,555 PERV_Q4VFZ2_3mut GSSGGGPAP 13,556 FLV_P10273_3mutA GSSEAAAKGGG 13,557 KORV_Q9TTC1-Pro_3mut EAAAKEAAAKEAAAKEAAAKEAAAKEAAAK 13,558 MLVCB_P08361_3mut GGSEAAAKPAP 13,559 MLVCB_P08361_3mut PAPAPAPAPAPAP 13,560 BAEVM_P10272_3mutA GGGGSEAAAKGGGGS 13,561 MLVMS_P03355_3mut EAAAKPAPGSS 13,562 MLVMS_P03355_3mut GSSGSSGSSGSSGSS 13,563 MLVBM_Q7SVK7_3mutA_WS PAPEAAAKGSS 13,564 MLVAV_P03356_3mut AEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKEAAAKA 13,565 AVIRE_P03360_3mut AEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKEAAAKA 13,566 PERV_Q4VFZ2_3mut GGSEAAAKGGG 13,567 PERV_Q4VFZ2_3mutA_WS GGSGGGGSS 13,568 MLVFF_P26809_3mutA PAPEAAAKGSS 13,569 MLVCB_P08361_3mut GGG PERV_Q4VFZ2_3mutA_WS GGSGGGEAAAK 13,571 MLVMS_P03355_3mut EAAAKGGGGSS 13,572 WMSV_P03359_3mut GSSPAPGGG 13,573 WMSV_P03359_3mutA EAAAKGSSGGG 13,574 PERV_Q4VFZ2_3mut GGSGGGEAAAK 13,575 PERV_Q4VFZ2_3mutA_WS GGSGGSGGSGGSGGS 13,576 PERV_Q4VFZ2_3mutA_WS EAAAKPAPGGS 13,577 PERV_Q4VFZ2_3mutA_WS GGGGGSEAAAK 13,578 PERV_Q4VFZ2_3mutA_WS GSSPAP 13,579 MLVFF_P26809_3mut GGGEAAAKPAP 13,580 AVIRE_P03360_3mut GSSGGSEAAAK 13,581 MLVMS_P03355_PLV919 EAAAKPAPGGS 13,582 WMSV_P03359_3mutA PAPGGG 13,583 KORV_Q9TTC1_3mutA EAAAKGSSPAP 13,584 KORV_Q9TTC1-Pro_3mut GSSPAPEAAAK 13,585 MLVFF_P26809_3mut GGSGGGEAAAK 13,586 MLVFF_P26809_3mutA GSSGSSGSS 13,587 WMSV_P03359_3mutA EAAAKGGS 13,588 BAEVM_P10272_3mut EAAAKPAPGGS 13,589 KORV_Q9TTC1_3mutA EAAAKPAPGGS 13,590 BAEVM_P10272_3mutA GSSGGGGGS 13,591 PERV_Q4VFZ2_3mut PAPGGGGSS 13,592 PERV_Q4VFZ2_3mut GSSGSSGSS 13,593 WMSV_P03359_3mut EAAAKEAAAKEAAAKEAAAK 13,594 WMSV_P03359_3mut GGS AVIRE_P03360_3mut EAAAKPAPGSS 13,596 MLVFF_P26809_3mut EAAAKGGG 13,597 KORV_Q9TTC1_3mut PAPGSSEAAAK 13,598 MLVMS_P03355_3mut PAPGSSGGS 13,599 MLVMS_P03355_PLV919 GSSPAPEAAAK 13,600 MLVMS_P03355_3mut GSSGSSGSSGSSGSSGSS 13,601 WMSV_P03359_3mutA GGGGS 13,602 BAEVM_P10272_3mut GSSPAP 13,603 MLVMS_P03355_3mut EAAAKGGGGSEAAAK 13,604 KORV_Q9TTC1-Pro_3mutA EAAAKEAAAK 13,605 WMSV_P03359_3mutA GGGGSSGGS 13,606 MLVCB_P08361_3mutA PAPGGSEAAAK 13,607 BAEVM_P10272_3mut EAAAKGGSPAP 13,608 MLVFF_P26809_3mut GSSGGSGGG 13,609 MLVBM_Q7SVK7_3mutA_WS GSSGGS 13,610 PERV_Q4VFZ2_3mut PAPGGSGSS 13,611 PERV_Q4VFZ2_3mutA_WS EAAAKGGSGSS 13,612 KORV_Q9TTC1-Pro_3mutA PAPAP 13,613 MLVCB_P08361_3mut EAAAKGSSPAP 13,614 PERV_Q4VFZ2_3mutA_WS EAAAKPAPGGG 13,615 MLVMS_P03355_PLV919 GGGGSGGGGSGGGGSGGGGSGGGGSGGGGS 13,616 MLVBM_Q7SVK7_3mut EAAAKGGGGSS 13,617 MLVMS_P03355_PLV919 PAPEAAAK 13,618 PERV_Q4VFZ2_3mut EAAAKPAPGSS 13,619 BAEVM_P10272_3mutA GGSPAP 13,620 PERV_Q4VFZ2_3mutA_WS GGSGGS 13,621 BAEVM_P10272_3mutA PAPEAAAKGSS 13,622 KORV_Q9TTC1_3mut PAPGSS 13,623 MLVMS_P03355_PLV919 PAPAPAPAPAP 13,624 MLVAV_P03356_3mutA GGG XMRV6_A1Z651_3mutA GGGPAP 13,626 PERV_Q4VFZ2_3mutA_WS GSSPAPEAAAK 13,627 KORV_Q9TTC1_3mutA PAP BAEVM_P10272_3mutA GGSPAP 13,629 BAEVM_P10272_3mutA PAPEAAAKGGS 13,630 MLVMS_P03355_PLV919 PAPGSSGGS 13,631 PERV_Q4VFZ2_3mutA_WS PAPAPAPAPAPAP 13,632 PERV_Q4VFZ2_3mut EAAAKEAAAKEAAAK 13,633 MLVCB_P08361_3mut GGSGGSGGSGGSGGS 13,634 MLVMS_P03355_PLV919 EAAAKPAPGGS 13,635 MLVMS_P03355_3mut GGSGGS 13,636 MLVMS_P03355_PLV919 EAAAKPAP 13,637 MLVMS_P03355_3mutA_WS GGSEAAAK 13,638 XMRV6_A1Z651_3mutA GGSGGG 13,639 KORV_Q9TTC1_3mut GGSGGGEAAAK 13,640 PERV_Q4VFZ2_3mut PAPEAAAKGGG 13,641 AVIRE_P03360 PAPAP 13,642 PERV_Q4VFZ2_3mut GSS KORV_Q9TTC1-Pro_3mutA EAAAKGSSGGG 13,644 MLVAV_P03356_3mutA GGSPAPGSS 13,645 MLVBM_Q7SVK7_3mutA_WS PAPEAAAK 13,646 MLVAV_P03356_3mut EAAAKGGSPAP 13,647 BAEVM_P10272_3mutA PAPAPAPAP 13,648 WMSV_P03359_3mutA PAPGGSEAAAK 13,649 MLVMS_P03355_3mut GGSGGSGGSGGS 13,650 WMSV_P03359_3mut GGGGGSGSS 13,651 XMRV6_A1Z651_3mut PAPGGSGGG 13,652 KORV_Q9TTC1_3mutA GGS MLVMS_P03355_3mut EAAAK 13,654 WMSV_P03359_3mut GGGEAAAKGSS 13,655 MLVBM_Q7SVK7_3mutA_WS GGSPAPGSS 13,656 MLVCB_P08361_3mut GGSEAAAKPAP 13,657 PERV_Q4VFZ2_3mut GGGGSGGGGSGGGGSGGGGSGGGGS 13,658 MLVCB_P08361_3mutA GGSGSS 13,659 BAEVM_P10272_3mutA GGGEAAAKGSS 13,660 WMSV_P03359_3mutA EAAAKGGSPAP 13,661 WMSV_P03359_3mut GSSPAPEAAAK 13,662 MLVMS_P03355_3mut GGSGGSGGSGGS 13,663 MLVMS_P03355_PLV919 GSSPAPEAAAK 13,664 WMSV_P03359_3mut GSSGSSGSSGSS 13,665 PERV_Q4VFZ2 GGSGSSEAAAK 13,666 WMSV_P03359_3mutA GGSGGG 13,667 MLVFF_P26809_3mut GGSPAPGGG 13,668 MLVFF_P26809_3mut GGSGGSGGS 13,669 BAEVM_P10272_3mutA GGGGSSEAAAK 13,670 MLVBM_Q7SVK7_3mut GGSPAPGSS 13,671 MLVMS_P03355_3mut EAAAKPAPGSS 13,672 AVIRE_P03360_3mut GGGGSSGGS 13,673 FLV_P10273_3mutA GGSPAPEAAAK 13,674 PERV_Q4VFZ2_3mut GGSEAAAK 13,675 MLVMS_P03355_3mutA_WS GSSGSSGSSGSS 13,676 MLVCB_P08361_3mutA EAAAKEAAAKEAAAKEAAAKEAAAK 13,677 MLVMS_P03355_PLV919 GGGGG 13,678 PERV_Q4VFZ2_3mut GGSEAAAKGSS 13,679 MLVCB_P08361_3mutA GSSGGG 13,680 MLVBM_Q7SVK7_3mutA_WS PAPGSSGGG 13,681 KORV_Q9TTC1-Pro_3mutA GGSGGS 13,682 BAEVM_P10272_3mut EAAAKGGGGGS 13,683 MLVBM_Q7SVK7_3mutA_WS GGSGSSPAP 13,684 MLVCB_P08361_3mut PAPGSSGGG 13,685 KORV_Q9TTC1 PAPGGSGGG 13,686 MLVMS_P03355_3mut GGGG 13,687 WMSV_P03359_3mutA EAAAKGGSPAP 13,688 MLVCB_P08361_3mut GSSGSS 13,689 FLV_P10273_3mutA GGSEAAAKPAP 13,690 SFV3L_P27401_2mut EAAAKGSSGGS 13,691 MLVAV_P03356_3mutA AEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKEAAAKA 13,692 MLVAV_P03356_3mutA EAAAKGGSGSS 13,693 PERV_Q4VFZ2_3mutA_WS GGGGG 13,694 MLVCB_P08361_3mut GGGEAAAK 13,695 BAEVM_P10272_3mut GGSGGSGGSGGS 13,696 MLVCB_P08361_3mut EAAAKEAAAKEAAAKEAAAKEAAAKEAAAK 13,697 PERV_Q4VFZ2 PAPAPAPAPAP 13,698 MLVMS_P03355_3mutA_WS EAAAKEAAAK 13,699 XMRV6_A1Z651_3mut GSSGGSEAAAK 13,700 PERV_Q4VFZ2_3mutA_WS PAPGGSEAAAK 13,701 KORV_Q9TTC1-Pro_3mutA EAAAKGGGPAP 13,702 MLVBM_Q7SVK7_3mutA_WS PAPGGSGSS 13,703 PERV_Q4VFZ2 SGSETPGTSESATPES 13,704 MLVMS_P03355_3mut GGSGGS 13,705 MLVMS_P03355_PLV919 EAAAKGGS 13,706 FLV_P10273_3mut GGSPAPGSS 13,707 MLVMS_P03355_3mutA_WS EAAAKEAAAKEAAAKEAAAK 13,708 FFV_093209_2mut GSSGGSGGG 13,709 MLVMS_P03355_3mutA_WS PAPGSSEAAAK 13,710 WMSV_P03359_3mut PAPAPAPAPAPAP 13,711 KORV_Q9TTC1_3mutA GGGGSS 13,712 BAEVM_P10272_3mut GGGGSEAAAKGGGGS 13,713 AVIRE_P03360_3mut GSSPAPEAAAK 13,714 KORV_Q9TTC1-Pro_3mutA PAPEAAAKGGG 13,715 MLVBM_Q7SVK7_3mut EAAAKEAAAK 13,716 WMSV_P03359_3mut EAAAK 13,717 SFV3L_P27401-Pro_2mutA GSSGGSGGG 13,718 XMRV6_A1Z651_3mutA GGGEAAAKPAP 13,719 WMSV_P03359_3mutA GGSGGS 13,720 MLVFF_P26809_3mutA EAAAKEAAAKEAAAKEAAAKEAAAKEAAAK 13,721 FOAMV_P14350_2mutA GGGGG 13,722 MLVAV_P03356_3mutA GSSGGSEAAAK 13,723 BAEVM_P10272_3mut SGGSSGGSSGSETPGTSESATPESSGGSSGGSS 13,724 SFV1_P23074 GGSGGGPAP 13,725 MLVCB_P08361_3mut GGSGSS 13,726 PERV_Q4VFZ2_3mut SGSETPGTSESATPES 13,727 MLVFF_P26809_3mut EAAAKGGSPAP 13,728 MLVMS_P03355_3mut PAPAP 13,729 PERV_Q4VFZ2_3mut AEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKEAAAKA 13,730 MLVBM_Q7SVK7_3mut GGGGGS 13,731 BAEVM_P10272_3mutA EAAAKEAAAK 13,732 AVIRE_P03360_3mut GSSGGSEAAAK 13,733 PERV_Q4VFZ2_3mut GGGEAAAK 13,734 WMSV_P03359_3mut GSSGGGEAAAK 13,735 AVIRE_P03360_3mutA GGG XMRV6_A1Z651_3mut GGGGSEAAAKGGGGS 13,737 BAEVM_P10272_3mut GGGG 13,738 MLVMS_P03355_3mut GGSGGS 13,739 MLVMS_P03355_3mutA_WS GGSGGGGSS 13,740 MLVBM_Q7SVK7_3mutA_WS GSSPAPGGS 13,741 PERV_Q4VFZ2_3mut GSSPAPEAAAK 13,742 PERV_Q4VFZ2_3mutA_WS EAAAKGGS 13,743 WMSV_P03359_3mut GGSGGSGGSGGS 13,744 PERV_Q4VFZ2_3mut GGGGSSEAAAK 13,745 KORV_Q9TTC1-Pro_3mut PAPAPAPAPAPAP 13,746 MLVAV_P03356_3mut EAAAKGSSGGG 13,747 MLVMS_P03355_PLV919 GGGGG 13,748 MLVBM_Q7SVK7_3mutA_WS AEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKEAAAKA 13,749 FFV_093209_2mutA SGGSSGGSSGSETPGTSESATPESSGGSSGGSS 13,750 KORV_Q9TTC1-Pro_3mut GGSPAPGGG 13,751 MLVMS_P03355_3mutA_WS GGGEAAAKGGS 13,752 MLVMS_P03355_3mut GGGEAAAK 13,753 PERV_Q4VFZ2_3mut PAPEAAAKGGG 13,754 MLVMS_P03355_3mut GSSGSSGSSGSSGSSGSS 13,755 BAEVM_P10272_3mutA AEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKEAAAKA 13,756 GALV_P21414_3mutA EAAAKGGSPAP 13,757 FFV_093209-Pro EAAAKEAAAK 13,758 MLVFF_P26809_3mut GGGGSGGGGSGGGGSGGGGGGGGSGGGGS 13,759 PERV_Q4VFZ2_3mutA_WS GGSGGSGGSGGS 13,760 MLVAV_P03356_3mutA EAAAKEAAAKEAAAKEAAAKEAAAK 13,761 SFV3L_P27401_2mutA GSSGSSGSSGSSGSSGSS 13,762 BAEVM_P10272_3mut GGGGS 13,763 MLVMS_P03355_PLV919 AEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKEAAAKA 13,764 SFV1_P23074 GGGGSGGGGS 13,765 KORV_Q9TTC1-Pro_3mutA GGGGSGGGGS 13,766 MLVMS_P03355_3mut GGSGSS 13,767 KORV_Q9TTC1_3mutA GSSPAPGGG 13,768 PERV_Q4VFZ2_3mut GSSGGSPAP 13,769 PERV_Q4VFZ2_3mutA_WS PAPGGS 13,770 PERV_Q4VFZ2_3mutA_WS GGSPAPEAAAK 13,771 FOAMV_P14350_2mutA GGGPAPGGS 13,772 SFV3L_P27401_2mut PAPGSSGGG 13,773 MLVCB_P08361_3mut GSSGGGEAAAK 13,774 AVIRE_P03360_3mut GSSGGG 13,775 XMRV6_A1Z651_3mut GSSGSS 13,776 PERV_Q4VFZ2_3mut GSSGGG 13,777 MLVAV_P03356_3mutA PAPGGGGGS 13,778 PERV_Q4VFZ2_3mut GSSEAAAK 13,779 MLVMS_P03355_3mut PAPGGG 13,780 FLV_P10273_3mutA GGGGSGGGGS 13,781 PERV_Q4VFZ2_3mut GSSGGS 13,782 MLVMS_P03355_PLV919 GGGGSGGGGS 13,783 SFV3L_P27401_2mut EAAAKGGSGSS 13,784 FLV_P10273_3mutA GSSEAAAKGGS 13,785 MLVMS_P03355_3mutA_WS PAPGSSEAAAK 13,786 SFV3L_P27401_2mutA GGGGSGGGGS 13,787 SFV3L_P27401-Pro_2mutA PAPGSSEAAAK 13,788 PERV_Q4VFZ2_3mut PAPGSSEAAAK 13,789 PERV_Q4VFZ2 GGSPAPGGG 13,790 AVIRE_P03360_3mut GGGGGS 13,791 PERV_Q4VFZ2_3mutA_WS GGGGSSGGS 13,792 PERV_Q4VFZ2_3mut PAPAPAPAP 13,793 AVIRE_P03360_3mutA GGSGGS 13,794 WMSV_P03359_3mutA GGGPAPGGS 13,795 PERV_Q4VFZ2_3mut GGSGGSGGSGGSGGS 13,796 MLVMS_P03355_PLV919 GGSGGG 13,797 PERV_Q4VFZ2_3mut EAAAKEAAAK 13,798 SFV3L_P27401_2mut PAPGSS 13,799 XMRV6_A1Z651_3mut GSSEAAAK 13,800 MLVFF_P26809_3mut GGSPAPGGG 13,801 MLVMS_P03355_3mut EAAAKGGG 13,802 WMSV_P03359_3mutA GSSEAAAKGGS 13,803 PERV_Q4VFZ2_3mutA_WS GSSGGSPAP 13,804 FFV_093209 GGGGGS 13,805 KORV_Q9TTC1-Pro_3mut GSSGGG 13,806 MLVCB_P08361_3mut GSSGSS 13,807 MLVCB_P08361_3mutA GGSEAAAKPAP 13,808 BAEVM_P10272_3mut EAAAKGGGGSS 13,809 MLVCB_P08361_3mut EAAAKPAPGGS 13,810 KORV_Q9TTC1-Pro_3mutA GSSGSSGSSGSSGSS 13,811 MLVAV_P03356_3mutA GGGGSEAAAKGGGGS 13,812 PERV_Q4VFZ2_3mutA_WS GGSGSS 13,813 KORV_Q9TTC1-Pro_3mut GSS SFV3L_P27401-Pro_2mutA PAPAP 13,815 BAEVM_P10272_3mut EAAAKPAP 13,816 BAEVM_P10272 EAAAKEAAAKEAAAKEAAAKEAAAK 13,817 KORV_Q9TTC1-Pro_3mut GGGGGGG 13,818 PERV_Q4VFZ2_3mutA_WS GGGGS 13,819 MLVMS_P03355_3mut GSSGGG 13,820 FLV_P10273_3mutA PAPAPAPAPAP 13,821 FLV_P10273_3mut EAAAKEAAAKEAAAK 13,822 WMSV_P03359_3mutA GSSGGS 13,823 MLVBM_Q7SVK7_3mutA_WS EAAAKPAPGGG 13,824 MLVMS_P03355_3mut GSSPAPGGS 13,825 WMSV_P03359_3mut PAPGSSGGG 13,826 PERV_Q4VFZ2_3mutA_WS GSSGGG 13,827 AVIRE_P03360_3mutA PAPGGSGSS 13,828 MLVFF_P26809_3mut PAPGSS 13,829 PERV_Q4VFZ2_3mut GGGGGSGSS 13,830 WMSV_P03359_3mutA EAAAKGGGGSS 13,831 MLVBM_Q7SVK7_3mutA_WS GGGGGGG 13,832 BAEVM_P10272_3mut PAPEAAAKGSS 13,833 MLVMS_P03355_3mut GGSGGGEAAAK 13,834 MLVMS_P03355_PLV919 EAAAKGGGGGS 13,835 MLVCB_P08361_3mut PAPGGS 13,836 KORV_Q9TTC1-Pro_3mut GGGG 13,837 FLV_P10273_3mutA EAAAKGGSGSS 13,838 MLVBM_Q7SVK7_3mutA_WS GGGGSSGGS 13,839 MLVMS_P03355_3mutA_WS GGGGGGGG 13,840 WMSV_P03359_3mut GGSGSSGGG 13,841 MLVMS_P03355_PLV919 GSSEAAAKGGS 13,842 KORV_Q9TTC1-Pro_3mutA EAAAKPAPGSS 13,843 MLVCB_P08361_3mut GGSPAPGSS 13,844 KORV_Q9TTC1_3mutA PAPGSSGGG 13,845 BAEVM_P10272_3mut EAAAKPAPGSS 13,846 WMSV_P03359_3mut GGSPAPEAAAK 13,847 XMRV6_A1Z651_3mutA GSSPAP 13,848 FLV_P10273_3mutA GSS BAEVM_P10272_3mutA EAAAKPAPGGS 13,850 FLV_P10273_3mutA GGSGSSPAP 13,851 FLV_P10273_3mutA PAPGSSGGS 13,852 MLVMS_P03355_3mut GSAGSAAGSGEF 13,853 PERV_Q4VFZ2_3mutA_WS GSSGGSEAAAK 13,854 KORV_Q9TTC1_3mutA GSSGGS 13,855 MLVMS_P03355_3mutA_WS EAAAKGGGGSEAAAK 13,856 SFV3L_P27401_2mut GSSGGS 13,857 PERV_Q4VFZ2_3mutA_WS GGSPAPEAAAK 13,858 FLV_P10273_3mut GGSEAAAKGSS 13,859 PERV_Q4VFZ2_3mutA_WS GSSPAPEAAAK 13,860 PERV_Q4VFZ2_3mutA_WS GGSGSSGGG 13,861 PERV_Q4VFZ2_3mut GGGG 13,862 AVIRE_P03360_3mutA GGSEAAAKPAP 13,863 WMSV_P03359_3mut GSSGGSPAP 13,864 MLVAV_P03356_3mutA GSSGGSEAAAK 13,865 MLVMS_P03355_3mut PAPEAAAKGGS 13,866 KORV_Q9TTC1-Pro_3mut GGSPAP 13,867 PERV_Q4VFZ2_3mutA_WS GGSEAAAK 13,868 MLVAV_P03356_3mutA EAAAKGGGGSEAAAK 13,869 KORV_Q9TTC1-Pro_3mut SGGSSGGSSGSETPGTSESATPESSGGSSGGSS 13,870 MLVMS_P03355_PLV919 GSSEAAAK 13,871 KORV_Q9TTC1_3mutA GGG AVIRE_P03360 GGSEAAAKGSS 13,873 MLVBM_Q7SVK7_3mut GGSEAAAKGSS 13,874 MLVMS_P03355_3mut GGSPAPEAAAK 13,875 MLVCB_P08361_3mut GGSGGGEAAAK 13,876 MLVCB_P08361_3mut GGSEAAAKPAP 13,877 MLVMS_P03355_3mutA_WS EAAAKGGSGSS 13,878 KORV_Q9TTC1-Pro_3mut GGGEAAAKGGS 13,879 MLVCB_P08361_3mut EAAAKGGGGSEAAAK 13,880 FLV_P10273_3mutA GGSPAP 13,881 MLVFF_P26809_3mut GGGGSSGGS 13,882 XMRV6_A1Z651_3mutA PAP MLVCB_P08361_3mut GGS SFV3L_P27401-Pro_2mutA GGGGSGGGGS 13,885 MLVMS_P03355_3mut GGGEAAAKGGS 13,886 MLVAV_P03356_3mutA GSSGSSGSSGSSGSSGSS 13,887 MLVMS_P03355_PLV919 PAPGSS 13,888 MLVCB_P08361_3mut GGSGGSGGS 13,889 MLVMS_P03355_PLV919 PAPGGSGGG 13,890 FLV_P10273_3mutA GGGGSGGGGSGGGGS 13,891 FLV_P10273_3mut GGSGSSGGG 13,892 KORV_Q9TTC1-Pro_3mutA GGSGGSGGS 13,893 GALV_P21414_3mutA GGGEAAAKGGS 13,894 WMSV_P03359_3mut SGSETPGTSESATPES 13,895 KORV_Q9TTC1_3mutA EAAAKGGGGGS 13,896 KORV_Q9TTC1-Pro_3mut EAAAKGSSPAP 13,897 BAEVM_P10272_3mut GGGG 13,898 MLVCB_P08361_3mut GGGGSGGGGSGGGGSGGGGSGGGGS 13,899 MLVBM_Q7SVK7_3mut GSSGGSGGG 13,900 MLVMS_P03355_PLV919 GGSGSS 13,901 MLVFF_P26809_3mut EAAAKGGS 13,902 AVIRE_P03360_3mutA GSSEAAAKGGS 13,903 MLVBM_Q7SVK7_3mutA_WS EAAAKPAPGGG 13,904 WMSV_P03359_3mut PAPGSSGGG 13,905 MLVCB_P08361_3mutA GGGGSSEAAAK 13,906 KORV_Q9TTC1-Pro_3mutA GSSEAAAKPAP 13,907 BAEVM_P10272_3mutA PAPGGGEAAAK 13,908 MLVBM_Q7SVK7_3mutA_WS GGSGGGEAAAK 13,909 MLVCB_P08361_3mutA GGGGGGGGSGGGGSGGGGSGGGGSGGGGS 13,910 FFV_093209 EAAAKGGGGGS 13,911 GALV_P21414_3mutA GGSPAPGGG 13,912 MLVMS_P03355_3mut GSSGSSGSS 13,913 FLV_P10273_3mutA EAAAK 13,914 MLVBM_Q7SVK7_3mut GGGGSSGGS 13,915 MLVMS_P03355_3mut GGSGSSPAP 13,916 PERV_Q4VFZ2_3mut EAAAKEAAAKEAAAKEAAAK 13,917 BAEVM_P10272_3mut GGGPAPGSS 13,918 MLVMS_P03355_3mut GSSPAPGGS 13,919 PERV_Q4VFZ2_3mutA_WS PAPAP 13,920 FLV_P10273_3mutA PAPAPAPAP 13,921 PERV_Q4VFZ2_3mut GGGGGSEAAAK 13,922 GALV_P21414_3mutA GGGGGSGSS 13,923 BAEVM_P10272_3mutA GGGEAAAKGSS 13,924 KORV_Q9TTC1_3mutA GGGGGSPAP 13,925 AVIRE_P03360_3mut GGGGGSEAAAK 13,926 SFV3L_P27401_2mutA GGS KORV_Q9TTC1_3mutA GGGGGGG 13,928 PERV_Q4VFZ2_3mut SGSETPGTSESATPES 13,929 SFV3L_P27401_2mutA EAAAKGGSGGG 13,930 MLVMS_P03355_3mut GGGGS 13,931 MLVFF_P26809_3mut EAAAKGSSGGG 13,932 BAEVM_P10272_3mut EAAAKPAPGGS 13,933 MLVF5_P26810_3mutA SGGSSGGSSGSETPGTSESATPESSGGSSGGSS 13,934 SFV3L_P27401_2mutA GGSPAPGGG 13,935 WMSV_P03359_3mutA GSAGSAAGSGEF 13,936 MLVFF_P26809_3mut GGGGSSGGS 13,937 MLVMS_P03355_3mutA_WS GGGGGGG 13,938 MLVCB_P08361_3mut GSSEAAAK 13,939 WMSV_P03359_3mut PAPGSS 13,940 FLV_P10273_3mutA GSSGGG 13,941 PERV_Q4VFZ2_3mutA_WS PAPGGG 13,942 MLVFF_P26809_3mut GGGGGSPAP 13,943 MLVMS_P03355_3mut GGSEAAAK 13,944 XMRV6_A1Z651_3mut GSSGGG 13,945 PERV_Q4VFZ2_3mut GGSGGSGGSGGS 13,946 MLVMS_P03355_3mut PAPAP 13,947 AVIRE_P03360_3mut GGSEAAAK 13,948 PERV_Q4VFZ2_3mut GGGGS 13,949 MLVMS_P03355_PLV919 GGGG 13,950 BAEVM_P10272_3mutA EAAAKGGGGSS 13,951 MLVCB_P08361_3mutA EAAAKEAAAKEAAAK 13,952 GALV_P21414_3mutA PAPGGGEAAAK 13,953 KORV_Q9TTC1 EAAAKGGSPAP 13,954 MLVMS_P03355_3mut GGSGSSEAAAK 13,955 MLVMS_P03355_3mut GGSPAPEAAAK 13,956 FLV_P10273_3mutA GGGGGGG 13,957 PERV_Q4VFZ2_3mut EAAAKEAAAKEAAAKEAAAKEAAAKEAAAK 13,958 SFV1_P23074_2mutA EAAAKGSSGGS 13,959 MLVMS_P03355_3mut GSSEAAAKPAP 13,960 MLVFF_P26809_3mut GGGGSS 13,961 FLV_P10273_3mutA EAAAKGGSGGG 13,962 AVIRE_P03360_3mutA GGSGGS 13,963 PERV_Q4VFZ2_3mutA_WS GGGGGSPAP 13,964 AVIRE_P03360_3mutA EAAAKEAAAKEAAAK 13,965 XMRV6_A1Z651_3mut PAPEAAAKGGS 13,966 FLV_P10273_3mutA GSSGGSEAAAK 13,967 MLVCB_P08361_3mut EAAAKGGSGGG 13,968 MLVMS_P03355 GGSGGGPAP 13,969 MLVMS_P03355_3mut GGS XMRV6_A1Z651_3mut GGSEAAAKPAP 13,971 MLVFF_P26809_3mut EAAAKGGG 13,972 MLVMS_P03355_PLV919 GSSGSSGSSGSS 13,973 WMSV_P03359_3mut GGSGSSPAP 13,974 PERV_Q4VFZ2_3mut GGGEAAAK 13,975 MLVMS_P03355_3mutA_WS GSSPAPGGS 13,976 KORV_Q9TTC1-Pro_3mutA GSSEAAAKGGG 13,977 SFV3L_P27401_2mut EAAAKPAPGGS 13,978 MLVCB_P08361_3mut GGSGGGEAAAK 13,979 PERV_Q4VFZ2 GGSGSS 13,980 MLVCB_P08361_3mut GGSGGGEAAAK 13,981 MLVBM_Q7SVK7_3mutA_WS GGSGGSGGSGGSGGSGGS 13,982 FLV_P10273_3mut PAPEAAAKGSS 13,983 MLVMS_P03355_3mut EAAAKGSSGGS 13,984 WMSV_P03359_3mutA GGSGSSEAAAK 13,985 MLVCB_P08361_3mut GGSGSSEAAAK 13,986 KORV_Q9TTC1_3mutA GSSGGSGGG 13,987 MLVMS_P03355_PLV919 EAAAKGGSGGG 13,988 SFV3L_P27401-Pro_2mutA GGSGGS 13,989 AVIRE_P03360_3mutA GSAGSAAGSGEF 13,990 MLVMS_P03355_PLV919 GGSGSS 13,991 GALV_P21414_3mutA GGGG 13,992 MLVFF_P26809_3mutA GGGGSGGGGSGGGGSGGGGS 13,993 WMSV_P03359_3mut SGSETPGTSESATPES 13,994 BAEVM_P10272_3mut EAAAKEAAAKEAAAKEAAAK 13,995 FOAMV_P14350_2mutA GGGEAAAKGGS 13,996 FLV_P10273_3mutA GSSGGSEAAAK 13,997 MLVFF_P26809_3mut EAAAKGGGGSS 13,998 MLVAV_P03356_3mut PAPGGSEAAAK 13,999 KORV_Q9TTC1-Pro_3mut EAAAK 14,000 XMRV6_A1Z651_3mut GSSGSSGSSGSSGSSGSS 14,001 PERV_Q4VFZ2_3mut GGGG 14,002 MLVCB_P08361_3mutA GSSGSS 14,003 WMSV_P03359_3mutA GSSGGSPAP 14,004 AVIRE_P03360_3mut GGSGGSGGS 14,005 MLVCB_P08361_3mut EAAAKGGGPAP 14,006 FLV_P10273_3mutA GGGGSGGGGS 14,007 MLVCB_P08361_3mut GGSEAAAKGSS 14,008 PERV_Q4VFZ2_3mutA_WS EAAAKEAAAKEAAAKEAAAKEAAAKEAAAK 14,009 SFV3L_P27401_2mutA GGSGSSEAAAK 14,010 PERV_Q4VFZ2_3mutA_WS EAAAKEAAAKEAAAKEAAAK 14,011 SFV3L_P27401-Pro_2mutA GSSEAAAKGGS 14,012 FLV_P10273_3mutA GGSGSS 14,013 PERV_Q4VFZ2 GGSGSSEAAAK 14,014 SFV3L_P27401-Pro_2mutA GSSGSSGSS 14,015 XMRV6_A1Z651_3mutA EAAAKGSSPAP 14,016 KORV_Q9TTC1_3mutA EAAAKPAP 14,017 FLV_P10273_3mutA GGSGSSEAAAK 14,018 KORV_Q9TTC1-Pro_3mut GGGGSGGGGSGGGGSGGGGSGGGGSGGGGS 14,019 KORV_Q9TTC1_3mutA GGGGSGGGGSGGGGS 14,020 KORV_Q9TTC1-Pro_3mutA GGGGGGG 14,021 FLV_P10273_3mut EAAAKGSS 14,022 WMSV_P03359_3mut EAAAKGGGPAP 14,023 MLVCB_P08361_3mut GSSGSS 14,024 MLVBM_Q7SVK7_3mutA_WS EAAAKGGGGGS 14,025 MLVFF_P26809_3mut GGSGGGEAAAK 14,026 FLV_P10273_3mutA PAPGSS 14,027 MLVFF_P26809_3mutA PAPGSS 14,028 BAEVM_P10272_3mutA GGSPAPGSS 14,029 AVIRE_P03360_3mut GGGGSSEAAAK 14,030 MLVMS_P03355_3mut GSSGGGGGS 14,031 FFV_093209-Pro EAAAKGSSPAP 14,032 PERV_Q4VFZ2_3mut GSSPAPGGS 14,033 PERV_Q4VFZ2_3mut GGGGGG 14,034 BAEVM_P10272_3mut EAAAKGGGGSS 14,035 PERV_Q4VFZ2_3mutA_WS PAPGGSEAAAK 14,036 KORV_Q9TTC1_3mutA SGGSSGGSSGSETPGTSESATPESSGGSSGGSS 14,037 MLVMS_P03355_3mutA_WS GSSGSSGSSGSS 14,038 MLVMS_P03355_3mut EAAAKGSSGGG 14,039 MLVMS_P03355_PLV919 GGSEAAAKPAP 14,040 AVIRE_P03360_3mutA GSSGSSGSSGSSGSS 14,041 WMSV_P03359_3mutA GGGEAAAKPAP 14,042 FLV_P10273_3mutA PAPGSSGGG 14,043 KORV_Q9TTC1_3mutA GSSGSS 14,044 MLVMS_P03355_3mutA_WS PAPEAAAK 14,045 BAEVM_P10272_3mut GGGPAPGSS 14,046 PERV_Q4VFZ2 GSSGGSPAP 14,047 MLVFF_P26809_3mut GGGGSS 14,048 SFV3L_P27401_2mut PAPEAAAKGSS 14,049 SFV3L_P27401_2mut GGSGGGPAP 14,050 XMRV6_A1Z651_3mutA PAPGGS 14,051 BAEVM_P10272_3mutA EAAAKGGGGGS 14,052 AVIRE_P03360_3mut GSSGGSPAP 14,053 KORV_Q9TTC1-Pro_3mutA GSSGGGGGS 14,054 WMSV_P03359_3mut GGGEAAAKGGS 14,055 AVIRE_P03360_3mut GGGEAAAKGSS 14,056 BAEVM_P10272_3mut PAPEAAAKGSS 14,057 MLVAV_P03356_3mutA GSSGSSGSSGSSGSS 14,058 MLVCB_P08361_3mut GGSPAPGSS 14,059 FLV_P10273_3mutA EAAAKGSSPAP 14,060 BAEVM_P10272_3mutA GGSGGSGGSGGSGGSGGS 14,061 PERV_Q4VFZ2 GGGGSSEAAAK 14,062 FLV_P10273_3mutA GGGGSSPAP 14,063 FFV_093209 GSSGGSPAP 14,064 MLVMS_P03355_3mut GGGPAPGSS 14,065 MLVMS_P03355_PLV919 PAPGSSGGS 14,066 PERV_Q4VFZ2_3mut GGGGGSPAP 14,067 MLVFF_P26809_3mut SGSETPGTSESATPES 14,068 MLVMS_P03355_3mutA_WS GSSGSSGSSGSSGSS 14,069 KORV_Q9TTC1_3mutA GSSPAPGGG 14,070 WMSV_P03359_3mut PAPAPAPAPAPAP 14,071 SFV3L_P27401_2mutA GGGPAPGGS 14,072 MLVMS_P03355_3mut PAPGGSEAAAK 14,073 WMSV_P03359_3mut GGGGSSEAAAK 14,074 FFV_093209-Pro GGSPAPGGG 14,075 FLV_P10273_3mutA GSSPAPEAAAK 14,076 AVIRE_P03360_3mut GGGEAAAK 14,077 FLV_P10273_3mutA PAPEAAAKGGG 14,078 MLVCB_P08361_3mut GGSPAPGGG 14,079 MLVCB_P08361_3mut GGSGGGGSS 14,080 BAEVM_P10272_3mutA GSSPAPEAAAK 14,081 MLVCB_P08361_3mut GGSPAPGGG 14,082 KORV_Q9TTC1-Pro_3mutA PAPGGSGSS 14,083 KORV_Q9TTC1_3mutA GSSPAP 14,084 KORV_Q9TTC1-Pro_3mutA SGSETPGTSESATPES 14,085 MLVMS_P03355 GSSGSSGSS 14,086 MLVAV_P03356_3mutA PAPGSSGGS 14,087 PERV_Q4VFZ2_3mutA_WS PAPGGS 14,088 KORV_Q9TTC1-Pro_3mutA PAPEAAAKGGG 14,089 SFV3L_P27401-Pro_2mutA GGSGGSGGS 14,090 BAEVM_P10272_3mut PAPGGS 14,091 MLVFF_P26809_3mut GSSGGSPAP 14,092 MLVMS_P03355_PLV919 GSSGGGGGS 14,093 FLV_P10273_3mutA GGGGGSPAP 14,094 KORV_Q9TTC1-Pro_3mut EAAAKPAPGSS 14,095 SFV3L_P27401-Pro_2mutA EAAAKGGSPAP 14,096 KORV_Q9TTC1-Pro GGGPAPEAAAK 14,097 MLVMS_P03355_PLV919 GGSEAAAKGSS 14,098 MLVMS_P03355 PAPEAAAKGSS 14,099 KORV_Q9TTC1_3mutA PAPEAAAKGGS 14,100 WMSV_P03359_3mutA GSSGGG 14,101 PERV_Q4VFZ2_3mutA_WS EAAAKGGGGSS 14,102 MLVMS_P03355_PLV919 EAAAKGGSPAP 14,103 AVIRE_P03360_3mutA GGGGSSGGS 14,104 MLVMS_P03355_PLV919 PAPEAAAKGSS 14,105 PERV_Q4VFZ2_3mutA_WS EAAAKGGGGGS 14,106 BAEVM_P10272_3mut GSSGGGGGS 14,107 MLVMS_P03355_3mut PAPAPAPAP 14,108 KORV_Q9TTC1_3mutA GGSGGSGGSGGS 14,109 MLVAV_P03356_3mut PAPAPAPAP 14,110 SFV3L_P27401_2mut GSSEAAAKPAP 14,111 MLVMS_P03355_3mut GGSGGGEAAAK 14,112 SFV3L_P27401_2mutA GSSGGSGGG 14,113 MLVMS_P03355_3mutA_WS GGGGGSPAP 14,114 MLVCB_P08361_3mutA GGGEAAAKGSS 14,115 XMRV6_A1Z651_3mutA GGGGSSPAP 14,116 BAEVM_P10272_3mut GGSGGG 14,117 PERV_Q4VFZ2_3mut GGGGSS 14,118 MLVBM_Q7SVK7_3mutA_WS EAAAKGSSGGS 14,119 PERV_Q4VFZ2_3mutA_WS GSSGGGGGS 14,120 PERV_Q4VFZ2 EAAAKGSSGGS 14,121 PERV_Q4VFZ2_3mut EAAAKEAAAK 14,122 MLVAV_P03356_3mut GSSGGGEAAAK 14,123 MLVAV_P03356_3mut GSSPAPGGG 14,124 XMRV6_A1Z651_3mut GGGGSGGGGSGGGGS 14,125 PERV_Q4VFZ2_3mut EAAAKEAAAKEAAAKEAAAK 14,126 KORV_Q9TTC1_3mutA EAAAKGGSGSS 14,127 MLVBM_Q7SVK7_3mut PAPEAAAK 14,128 BLVJ_P03361 GSSGGG 14,129 FFV_093209-Pro GGSGGGEAAAK 14,130 KORV_Q9TTC1-Pro_3mutA EAAAK 14,131 FLV_P10273_3mutA GGGGSSPAP 14,132 MLVMS_P03355_3mut GSS SFV3L_P27401-Pro_2mut PAPEAAAKGSS 14,134 BAEVM_P10272_3mut GGGGGSPAP 14,135 PERV_Q4VFZ2_3mut GSSGSSGSS 14,136 BAEVM_P10272_3mutA GGGGSGGGGSGGGGSGGGGS 14,137 SFV1_P23074_2mut GGGGSSEAAAK 14,138 SFV3L_P27401_2mutA GGGGSGGGGSGGGGSGGGGS 14,139 FOAMV_P14350-Pro_2mut PAPGSSEAAAK 14,140 MLVBM_Q7SVK7_3mutA_WS GGGGGSGSS 14,141 MLVFF_P26809_3mutA GGSEAAAKGGG 14,142 MLVBM_Q7SVK7_3mut PAPGSSGGG 14,143 PERV_Q4VFZ2 GGS PERV_Q4VFZ2_3mutA_WS EAAAKGGSGSS 14,145 FLV_P10273_3mut GGGEAAAK 14,146 WMSV_P03359_3mutA GGSEAAAKPAP 14,147 MLVBM_Q7SVK7_3mut SGSETPGTSESATPES 14,148 FOAMV_P14350-Pro_2mutA EAAAKPAPGGS 14,149 AVIRE_P03360_3mut EAAAKGGGGGS 14,150 KORV_Q9TTC1-Pro_3mutA GGGGS 14,151 PERV_Q4VFZ2_3mut GGSEAAAKGSS 14,152 MLVFF_P26809_3mutA GGSEAAAKGGG 14,153 AVIRE_P03360 GGSGGSGGSGGSGGSGGS 14,154 SFV3L_P27401_2mut GGSEAAAKGSS 14,155 SFV3L_P27401-Pro_2mutA GGGEAAAKPAP 14,156 MLVCB_P08361_3mut GGSEAAAK 14,157 MLVMS_P03355_PLV919 GGSPAPGSS 14,158 KORV_Q9TTC1-Pro_3mutA GSSPAPEAAAK 14,159 WMSV_P03359_3mutA GGSGSS 14,160 KORV_Q9TTC1-Pro_3mutA PAPGGGGGS 14,161 AVIRE_P03360_3mut PAPEAAAKGSS 14,162 FFV_093209-Pro GGSGGGEAAAK 14,163 WMSV_P03359_3mut PAPGGG 14,164 MLVMS_P03355_3mut EAAAKGGG 14,165 FLV_P10273_3mutA GSSGSSGSSGSS 14,166 MLVCB_P08361_3mut EAAAKGGSGGG 14,167 FFV_093209 GSSPAPGGS 14,168 PERV_Q4VFZ2_3mutA_WS GSSPAPGGS 14,169 MLVCB_P08361_3mut GGGPAP 14,170 WMSV_P03359_3mutA GGGPAP 14,171 KORV_Q9TTC1_3mutA GGSPAPGSS 14,172 KORV_Q9TTC1-Pro_3mut PAPAP 14,173 MLVMS_P03355_3mut GGGGGGG 14,174 MLVMS_P03355_3mut GGGGG 14,175 KORV_Q9TTC1-Pro_3mut GSAGSAAGSGEF 14,176 FOAMV_P14350_2mutA PAPAP 14,177 KORV_Q9TTC1-Pro_3mutA GGSEAAAKGGG 14,178 SFV3L_P27401-Pro_2mutA PAPAP 14,179 WMSV_P03359_3mut GGGGSGGGGSGGGGS 14,180 SFV3L_P27401_2mut PAPGGS 14,181 KORV_Q9TTC1_3mutA GGGEAAAKPAP 14,182 FLV_P10273_3mut GGGGGS 14,183 MLVAV_P03356_3mutA GSSEAAAKGGG 14,184 WMSV_P03359_3mut EAAAKGGGGSS 14,185 GALV_P21414_3mutA GSSGGS 14,186 MLVAV_P03356_3mutA GSSGGG 14,187 MLVBM_Q7SVK7_3mut PAPAPAP 14,188 SFV3L_P27401-Pro_2mutA GGGG 14,189 KORV_Q9TTC1_3mutA EAAAKPAPGGS 14,190 MLVFF_P26809_3mut GGGGSGGGGS 14,191 XMRV6_A1Z651_3mut EAAAKGGG 14,192 MLVCB_P08361_3mut GGGGSSPAP 14,193 KORV_Q9TTC1_3mutA GSSEAAAKGGG 14,194 KORV_Q9TTC1-Pro_3mutA GGGGG 14,195 BLVJ_P03361_2mutB GGGEAAAKGSS 14,196 FFV_093209-Pro GSSGSSGSS 14,197 BAEVM_P10272_3mut GSSGGSPAP 14,198 PERV_Q4VFZ2_3mut EAAAKGGS 14,199 KORV_Q9TTC1_3mut GGSPAPEAAAK 14,200 AVIRE_P03360_3mut GGSEAAAK 14,201 WMSV_P03359_3mut GSSGGS 14,202 KORV_Q9TTC1-Pro_3mutA GGGPAPEAAAK 14,203 KORV_Q9TTC1_3mutA PAPGSS 14,204 WMSV_P03359_3mutA GGSEAAAKGSS 14,205 FLV_P10273_3mutA EAAAKEAAAKEAAAKEAAAKEAAAK 14,206 SFV3L_P27401 GSSEAAAKGGG 14,207 SFV3L_P27401-Pro_2mutA GGGGSEAAAKGGGGS 14,208 KORV_Q9TTC1-Pro_3mutA GGSGGSGGS 14,209 WMSV_P03359_3mut GGGGGSGSS 14,210 KORV_Q9TTC1-Pro GGGGSGGGGSGGGGSGGGGS 14,211 MLVMS_P03355_3mut EAAAKGGG 14,212 PERV_Q4VFZ2 GGSEAAAKGGG 14,213 KORV_Q9TTC1-Pro_3mut GSSGGSGGG 14,214 PERV_Q4VFZ2_3mutA_WS GGGGGS 14,215 PERV_Q4VFZ2_3mut GSAGSAAGSGEF 14,216 PERV_Q4VFZ2 PAPEAAAKGSS 14,217 BAEVM_P10272_3mutA GSSPAPGGG 14,218 MLVCB_P08361_3mut GGGGSSPAP 14,219 KORV_Q9TTC1-Pro_3mutA PAPGGSGGG 14,220 MLVFF_P26809_3mut GSSPAP 14,221 KORV_Q9TTC1_3mutA PAPGSS 14,222 SFV3L_P27401-Pro_2mut GGSGGGGSS 14,223 MLVMS_P03355_PLV919 GSSGGS 14,224 WMSV_P03359_3mutA EAAAKGGGGGS 14,225 PERV_Q4VFZ2 GGGGG 14,226 KORV_Q9TTC1_3mutA EAAAKGSS 14,227 MLVMS_P03355_PLV919 EAAAKEAAAKEAAAKEAAAKEAAAK 14,228 FLV_P10273_3mut EAAAKEAAAKEAAAKEAAAK 14,229 SFV3L_P27401-Pro_2mut GSAGSAAGSGEF 14,230 SFV3L_P27401_2mutA GGGPAPGGS 14,231 FLV_P10273_3mutA GGSEAAAKGGG 14,232 MLVCB_P08361_3mut PAPGGGEAAAK 14,233 BAEVM_P10272_3mut EAAAKPAPGSS 14,234 FOAMV_P14350_2mut GGSEAAAK 14,235 KORV_Q9TTC1_3mutA GGSGSS 14,236 AVIRE_P03360 GGSPAPEAAAK 14,237 MLVMS_P03355_PLV919 GGGGS 14,238 XMRV6_A1Z651_3mut GGSPAPGGG 14,239 XMRV6_A1Z651_3mut EAAAKPAPGGS 14,240 PERV_Q4VFZ2 GSSPAP 14,241 BAEVM_P10272_3mut GGSGSSGGG 14,242 FLV_P10273_3mutA PAPGGG 14,243 PERV_Q4VFZ2_3mutA_WS GSSGGSEAAAK 14,244 MLVBM_Q7SVK7_3mut GGSEAAAK 14,245 MLVMS_P03355_3mut GGGPAPGGS 14,246 MLVFF_P26809_3mut GSAGSAAGSGEF 14,247 MLVBM_Q7SVK7_3mutA_WS EAAAKPAPGGS 14,248 SFVCP_Q87040 PAPGGG 14,249 PERV_Q4VFZ2_3mutA_WS GSSPAPEAAAK 14,250 MLVBM_Q7SVK7 PAPEAAAK 14,251 MLVBM_Q7SVK7_3mut PAPGGGGGS 14,252 AVIRE_P03360_3mutA GGSEAAAKPAP 14,253 MLVBM_Q7SVK7_3mut EAAAKGSS 14,254 WMSV_P03359_3mutA GGGEAAAK 14,255 MLVFF_P26809_3mutA EAAAKEAAAKEAAAK 14,256 MLVMS_P03355_3mut PAPEAAAKGGG 14,257 BAEVM_P10272_3mut PAPAPAP 14,258 MLVCB_P08361_3mut EAAAKPAPGGS 14,259 BAEVM_P10272_3mut GGGGGGGGS 14,260 FLV_P10273_3mut GGGGSEAAAKGGGGS 14,261 KORV_Q9TTC1_3mut EAAAK 14,262 FLV_P10273_3mut PAPAPAP 14,263 WMSV_P03359_3mut GGGGSEAAAKGGGGS 14,264 FFV_093209-Pro GGSPAPEAAAK 14,265 MLVMS_P03355_3mut GGSGSSGGG 14,266 XMRV6_A1Z651_3mut GGSPAPGSS 14,267 PERV_Q4VFZ2_3mut SGGSSGGSSGSETPGTSESATPESSGGSSGGSS 14,268 SFV3L_P27401-Pro_2mutA EAAAKGGGPAP 14,269 BAEVM_P10272_3mutA GSSGGSEAAAK 14,270 MLVMS_P03355_3mutA_WS SGSETPGTSESATPES 14,271 PERV_Q4VFZ2_3mutA_WS EAAAKEAAAKEAAAKEAAAKEAAAK 14,272 KORV_Q9TTC1-Pro_3mutA GSSGSSGSS 14,273 KORV_Q9TTC1_3mutA GSSPAPGGG 14,274 SFV3L_P27401-Pro_2mutA GSSGGGEAAAK 14,275 KORV_Q9TTC1_3mutA GGSGGGGSS 14,276 PERV_Q4VFZ2_3mutA_WS GSSGGGEAAAK 14,277 MLVCB_P08361_3mut GSSEAAAKGGG 14,278 MLVCB_P08361_3mut GGSGGGGSS 14,279 KORV_Q9TTC1_3mutA GGSGSSPAP 14,280 PERV_Q4VFZ2_3mutA_WS GSSPAP 14,281 MLVMS_P03355_3mut GGGGSSEAAAK 14,282 AVIRE_P03360 GGS WMSV_P03359_3mut EAAAKEAAAK 14,284 PERV_Q4VFZ2_3mut PAPAPAPAP 14,285 MLVAV_P03356_3mut GGSEAAAKGGG 14,286 KORV_Q9TTC1_3mutA PAPGGG 14,287 MLVAV_P03356_3mut EAAAKGSS 14,288 BAEVM_P10272_3mut GGGGSGGGGS 14,289 WMSV_P03359_3mutA GGSGGSGGS 14,290 SFV3L_P27401_2mut EAAAK 14,291 MLVCB_P08361_3mut GGGGSSGGS 14,292 WMSV_P03359_3mutA GGGPAPEAAAK 14,293 MLVAV_P03356_3mutA EAAAKEAAAKEAAAK 14,294 FFV_093209 GSSEAAAKGGG 14,295 MLVBM_Q7SVK7_3mut GGGPAPGGS 14,296 FLV_P10273_3mut GGSEAAAKGGG 14,297 WMSV_P03359_3mut EAAAKGGGGGS 14,298 XMRV6_A1Z651_3mutA EAAAKGGSGGG 14,299 FLV_P10273_3mutA GGSEAAAKGGG 14,300 SFV3L_P27401_2mutA GGGGS 14,301 PERV_Q4VFZ2_3mutA_WS GSSGGS 14,302 MLVMS_P03355_3mut GSSGSS 14,303 MLVAV_P03356_3mutA GGSPAPGGG 14,304 MLVBM_Q7SVK7_3mutA_WS GSSGGGGGS 14,305 MLVF5_P26810_3mut PAPAPAPAP 14,306 MLVCB_P08361_3mut PAPAP 14,307 PERV_Q4VFZ2_3mutA_WS PAPGSSGGS 14,308 KORV_Q9TTC1_3mut PAPGSSGGG 14,309 PERV_Q4VFZ2_3mut GGGEAAAK 14,310 MLVMS_P03355_PLV919 GGSGGSGGSGGSGGS 14,311 SFV3L_P27401-Pro_2mutA GGSGGG 14,312 FLV_P10273_3mut PAPEAAAKGGG 14,313 MLVFF_P26809_3mut PAP PERV_Q4VFZ2_3mutA_WS PAPGGSGSS 14,315 FFV_093209_2mut EAAAKEAAAKEAAAKEAAAKEAAAKEAAAK 14,316 FFV_093209-Pro_2mut GSSGSSGSSGSS 14,317 FFV_093209-Pro GSSGSSGSSGSSGSS 14,318 FLV_P10273_3mutA GGGEAAAKPAP 14,319 PERV_Q4VFZ2 PAPGSSGGG 14,320 SFV3L_P27401_2mut PAPGGSGSS 14,321 KORV_Q9TTC1-Pro_3mut PAPAPAPAPAP 14,322 GALV_P21414_3mutA GGSGGGEAAAK 14,323 PERV_Q4VFZ2_3mut GSSPAP 14,324 MLVCB_P08361_3mut EAAAKPAP 14,325 MLVF5_P26810_3mut GGGGSGGGGSGGGGSGGGGS 14,326 MLVBM_Q7SVK7_3mut GGSGGG 14,327 WMSV_P03359_3mut GGSGGSGGS 14,328 KORV_Q9TTC1_3mut GGGGGGGG 14,329 MLVFF_P26809_3mut GGGGSS 14,330 MLVAV_P03356_3mut GSSGGGGGS 14,331 SFV3L_P27401_2mut EAAAKEAAAKEAAAKEAAAKEAAAKEAAAK 14,332 GALV_P21414_3mutA GSSGSSGSS 14,333 PERV_Q4VFZ2_3mut GSSPAPGGS 14,334 MLVFF_P26809_3mut PAPAPAP 14,335 AVIRE_P03360_3mutA EAAAKEAAAKEAAAKEAAAK 14,336 WMSV_P03359_3mutA PAPAPAPAP 14,337 SFV3L_P27401_2mutA GGGGSS 14,338 MLVAV_P03356_3mutA GSSGSSGSSGSSGSS 14,339 SFV3L_P27401_2mutA PAPGGS 14,340 WMSV_P03359_3mutA GSSEAAAKGGG 14,341 PERV_Q4VFZ2 GSSGGSPAP 14,342 MLVMS_P03355_PLV919 GSSGSSGSSGSSGSSGSS 14,343 SFV3L_P27401_2mutA GGSGSSGGG 14,344 MLVCB_P08361_3mut GGGPAPGSS 14,345 SFV3L_P27401-Pro_2mutA GSSEAAAKGGS 14,346 WMSV_P03359_3mut GSSEAAAKGGG 14,347 MLVAV_P03356_3mut GGSGGGPAP 14,348 FFV_093209-Pro GSSGSS 14,349 PERV_Q4VFZ2_3mut PAPGGGGGS 14,350 GALV_P21414_3mutA EAAAKPAPGGS 14,351 MLVAV_P03356_3mut GSSGSS 14,352 MLVMS_P03355_3mut EAAAKPAPGGS 14,353 FFV_093209-Pro GGGPAPEAAAK 14,354 MLVMS_P03355_3mutA_WS GSSEAAAKGGG 14,355 MLVBM_Q7SVK7_3mut GGGEAAAKGGS 14,356 BAEVM_P10272_3mut GSSGSS 14,357 KORV_Q9TTC1-Pro_3mutA EAAAKEAAAKEAAAK 14,358 SFV1_P23074 PAPGSSGGS 14,359 KORV_Q9TTC1-Pro_3mut PAPAPAPAPAP 14,360 MLVMS_P03355 GSSEAAAK 14,361 SFV3L_P27401_2mut PAP PERV_Q4VFZ2_3mut GGSEAAAKGGG 14,363 MLVBM_Q7SVK7_3mut GGSGGGPAP 14,364 MLVBM_Q7SVK7_3mutA_WS GSSGSS 14,365 MLVMS_P03355_3mut GGSEAAAK 14,366 MLVMS_P03355 GSSEAAAKGGS 14,367 MLVMS_P03355_PLV919 PAPGGGGGS 14,368 MLVFF_P26809_3mut GSSGGG 14,369 PERV_Q4VFZ2_3mut GSSGGS 14,370 PERV_Q4VFZ2_3mutA_WS PAPGGG 14,371 BAEVM_P10272_3mut PAPGSSGGG 14,372 MLVBM_Q7SVK7_3mut GGSEAAAK 14,373 SFV3L_P27401_2mut GSSPAPEAAAK 14,374 SFV3L_P27401-Pro_2mut GSSGGSPAP 14,375 BAEVM_P10272_3mut GGSPAPGSS 14,376 PERV_Q4VFZ2_3mutA_WS GGSGGSGGS 14,377 PERV_Q4VFZ2 GGSGGGPAP 14,378 FLV_P10273_3mut GGGPAPEAAAK 14,379 SFV3L_P27401_2mutA GGGGS 14,380 FLV_P10273_3mutA GSSGGSGGG 14,381 XMRV6_A1Z651_3mut EAAAKGGGGSS 14,382 PERV_Q4VFZ2 GGSGSSGGG 14,383 SFV3L_P27401-Pro_2mutA GGSGGSGGS 14,384 MLVFF_P26809_3mut GGGPAPEAAAK 14,385 FLV_P10273_3mut GSSGGGEAAAK 14,386 MLVMS_P03355_3mut GGG SFV3L_P27401_2mut GSAGSAAGSGEF 14,388 WMSV_P03359_3mut GSSGGGPAP 14,389 MLVMS_P03355_PLV919 GGGGSS 14,390 KORV_Q9TTC1-Pro_3mut GGGGSSEAAAK 14,391 KORV_Q9TTC1 PAPGGSGGG 14,392 SFV3L_P27401_2mut GSSGSSGSSGSSGSS 14,393 FFV_093209 GSSGGSPAP 14,394 MLVMS_P03355_3mut GGSEAAAK 14,395 KORV_Q9TTC1-Pro_3mutA GGGGSGGGGS 14,396 BAEVM_P10272_3mut GSSEAAAKGGG 14,397 AVIRE_P03360_3mut EAAAKPAPGGG 14,398 FLV_P10273_3mut EAAAKGGSPAP 14,399 SFV3L_P27401-Pro_2mutA GSSEAAAKPAP 14,400 MLVBM_Q7SVK7_3mut GGGPAPGGS 14,401 MLVCB_P08361_3mut GGG SFV3L_P27401_2mutA EAAAKGGGGSEAAAK 14,403 SFV3L_P27401_2mutA GGSGSSGGG 14,404 MLVBM_Q7SVK7_3mut GSAGSAAGSGEF 14,405 BAEVM_P10272_3mut GGGEAAAK 14,406 FOAMV_P14350_2mutA PAPEAAAKGGS 14,407 WMSV_P03359_3mut PAPAPAPAPAPAP 14,408 MLVF5_P26810_3mutA GGSGGGGSS 14,409 FLV_P10273_3mutA PAPGSSGGS 14,410 BAEVM_P10272_3mut PAPEAAAK 14,411 WMSV_P03359_3mutA GSSGSSGSSGSSGSSGSS 14,412 FFV_093209-Pro_2mut GGGGGSGSS 14,413 FFV_093209-Pro GGGGGGGG 14,414 SFV3L_P27401-Pro_2mutA GGGGGG 14,415 FLV_P10273_3mut GSSGGSGGG 14,416 MLVAV_P03356_3mutA GGGGSS 14,417 SFV3L_P27401-Pro_2mutA GGSGGGPAP 14,418 FOAMV_P14350_2mut GSSGSS 14,419 AVIRE_P03360_3mutA EAAAKEAAAKEAAAKEAAAKEAAAK 14,420 SFV3L_P27401-Pro_2mutA EAAAKEAAAK 14,421 BAEVM_P10272_3mut GSSPAPEAAAK 14,422 GALV_P21414_3mutA GGSEAAAKPAP 14,423 SFV3L_P27401_2mutA GGSGGGEAAAK 14,424 SFV3L_P27401-Pro_2mutA EAAAKGSSPAP 14,425 FOAMV_P14350_2mut GGSGSSEAAAK 14,426 SFV3L_P27401_2mut GGG PERV_Q4VFZ2 GGGGGSGSS 14,428 FOAMV_P14350_2mut GGSGGGEAAAK 14,429 KORV_Q9TTC1-Pro_3mut GSSGGSGGG 14,430 AVIRE_P03360_3mutA EAAAKPAPGGG 14,431 SFV3L_P27401_2mutA PAPGGSGGG 14,432 KORV_Q9TTC1-Pro_3mut PAPAPAP 14,433 WMSV_P03359_3mutA GSSEAAAKPAP 14,434 SFV1_P23074 SGGSSGGSSGSETPGTSESATPESSGGSSGGSS 14,435 SRV2_P51517 GSSGGSGGG 14,436 PERV_Q4VFZ2_3mutA_WS GSSGSSGSSGSSGSSGSS 14,437 FFV_093209 GSSGGGPAP 14,438 WMSV_P03359_3mut PAPAPAPAPAPAP 14,439 MLVBM_Q7SVK7_3mut GGGGGSPAP 14,440 KORV_Q9TTC1-Pro_3mutA PAPGSS 14,441 MLVBM_Q7SVK7_3mutA_WS PAPEAAAKGGS 14,442 SFV3L_P27401-Pro_2mut GGGGSSPAP 14,443 MLVMS_P03355_3mut GGSEAAAK 14,444 FFV_093209-Pro EAAAKPAPGGS 14,445 AVIRE_P03360_3mutA PAPGSS 14,446 WMSV_P03359_3mut PAPGSSGGG 14,447 SFV3L_P27401-Pro_2mutA EAAAKEAAAKEAAAK 14,448 SFV3L_P27401_2mut GGS MLVRD_P11227_3mut GGGGS 14,450 KORV_Q9TTC1-Pro_3mut GGSGGGGSS 14,451 KORV_Q9TTC1 GGSGGG 14,452 MLVMS_P03355_3mutA_WS GGGEAAAKPAP 14,453 BAEVM_P10272_3mut EAAAKEAAAKEAAAKEAAAKEAAAK 14,454 FLV_P10273 PAPGGSGGG 14,455 KORV_Q9TTC1-Pro_3mutA GSSGSSGSSGSSGSSGSS 14,456 HTL1L_POC211 GGGEAAAKPAP 14,457 WMSV_P03359 GSSGGSPAP 14,458 FFV_093209-Pro PAPAPAPAPAP 14,459 SFV3L_P27401-Pro_2mutA GSSGGSEAAAK 14,460 SFV3L_P27401_2mutA GGSPAPGSS 14,461 SFV3L_P27401_2mut GGSGGSGGS 14,462 KORV_Q9TTC1-Pro_3mut PAPEAAAKGSS 14,463 KORV_Q9TTC1-Pro_3mut EAAAKGGS 14,464 KORV_Q9TTC1_3mutA EAAAKGGGGSEAAAK 14,465 SFV3L_P27401-Pro_2mut GGGGSSPAP 14,466 FFV_093209-Pro EAAAK 14,467 SFV3L_P27401_2mut EAAAKGGGGSS 14,468 BAEVM_P10272_3mut GGGGGSEAAAK 14,469 MLVBM_Q7SVK7_3mut GGGG 14,470 PERV_Q4VFZ2 GGGGGSEAAAK 14,471 FLV_P10273_3mut EAAAKGGGPAP 14,472 KORV_Q9TTC1-Pro GGGGSGGGGSGGGGSGGGGS 14,473 FFV_093209_2mutA GSSGGSGGG 14,474 PERV_Q4VFZ2_3mut GGGGSGGGGSGGGGS 14,475 GALV_P21414_3mutA GGSGGGEAAAK 14,476 AVIRE_P03360_3mutA PAPEAAAKGGG 14,477 SFV3L_P27401_2mut GGGGSGGGGS 14,478 AVIRE_P03360 GSSGGGEAAAK 14,479 SFV3L_P27401_2mutA GGGGG 14,480 AVIRE_P03360_3mutA GGSGSS 14,481 KORV_Q9TTC1_3mut PAPAPAPAPAPAP 14,482 FOAMV_P14350_2mut GGSEAAAKPAP 14,483 KORV_Q9TTC1-Pro_3mut GGGGGG 14,484 PERV_Q4VFZ2_3mut GSSGGGEAAAK 14,485 MLVBM_Q7SVK7 SGGSSGGSSGSETPGTSESATPESSGGSSGGSS 14,486 MLVAV_P03356 GGSPAPGSS 14,487 BAEVM_P10272_3mut GGGGSSPAP 14,488 BAEVM_P10272 GGGGSEAAAKGGGGS 14,489 SFV3L_P27401_2mut GGGGGGGG 14,490 GALV_P21414_3mutA PAPAP 14,491 MLVAV_P03356_3mut GGGEAAAK 14,492 PERV_Q4VFZ2_3mutA_WS GSSPAPGGG 14,493 FFV_093209_2mut GGSGGSGGSGGSGGS 14,494 BAEVM_P10272 GGGGGS 14,495 MLVF5_P26810_3mutA PAPGGGGSS 14,496 FLV_P10273_3mutA GGGEAAAK 14,497 MLVBM_Q7SVK7_3mut PAPEAAAKGGG 14,498 WMSV_P03359_3mut GSSEAAAK 14,499 MLVBM_Q7SVK7_3mut EAAAKEAAAK 14,500 AVIRE_P03360 EAAAKGGGGGS 14,501 MLVBM_Q7SVK7_3mut GGGEAAAKGGS 14,502 SFV3L_P27401-Pro_2mutA PAPAPAPAPAP 14,503 MLVF5_P26810_3mut PAPGSSEAAAK 14,504 SFV3L_P27401-Pro_2mutA EAAAKEAAAKEAAAK 14,505 BAEVM_P10272_3mutA GGSPAPGSS 14,506 MLVMS_P03355 PAPGSSGGS 14,507 FLV_P10273_3mutA EAAAKEAAAKEAAAKEAAAK 14,508 FOAMV_P14350-Pro_2mut EAAAKGGG 14,509 KORV_Q9TTC1_3mutA EAAAKGGSGGG 14,510 MLVBM_Q7SVK7_3mut GGGGGS 14,511 KORV_Q9TTC1-Pro_3mutA PAPGGSGGG 14,512 WMSV_P03359_3mut GGGPAPGGS 14,513 KORV_Q9TTC1_3mutA GSS FFV_093209 GGSGGSGGS 14,515 PERV_Q4VFZ2_3mut GGGGS 14,516 GALV_P21414_3mutA GGGG 14,517 MLVF5_P26810_3mut GGSEAAAKPAP 14,518 FFV_093209-Pro_2mut PAPAPAPAP 14,519 FFV_093209-Pro PAP MLVF5_P26810_3mut EAAAKEAAAKEAAAK 14,521 FFV_093209_2mut EAAAKGSS 14,522 MLVCB_P08361_3mut EAAAKGGG 14,523 MLVBM_Q7SVK7_3mut PAPEAAAKGGG 14,524 FFV_093209_2mut GSSGGGEAAAK 14,525 SFV1_P23074-Pro_2mut PAPGGGEAAAK 14,526 GALV_P21414_3mutA GGGGSGGGGSGGGGSGGGGS 14,527 FOAMV_P14350-Pro_2mutA GSSGGG 14,528 FOAMV_P14350_2mut GGGGSGGGGSGGGGSGGGGS 14,529 SFV3L_P27401_2mutA GGSGSS 14,530 AVIRE_P03360_3mut GGSGSSEAAAK 14,531 MMTVB_P03365_WS PAPAPAP 14,532 MLVAV_P03356_3mutA GSSGGSPAP 14,533 SFV3L_P27401-Pro_2mut GGSPAP 14,534 AVIRE_P03360 GGSGGGPAP 14,535 FFV_093209 GSSEAAAK 14,536 PERV_Q4VFZ2 GSSGGGPAP 14,537 PERV_Q4VFZ2_3mutA_WS GGGGSSEAAAK 14,538 KORV_Q9TTC1_3mutA GGSEAAAKPAP 14,539 SFVCP_Q87040 GGSGGGPAP 14,540 FOAMV_P14350_2mutA GGGGSGGGGSGGGGSGGGGS 14,541 BLVJ_P03361_2mutB GGGGSSPAP 14,542 SFV3L_P27401_2mutA EAAAKGGS 14,543 MLVF5_P26810_3mut GGSEAAAKGSS 14,544 MLVCB_P08361_3mut GGGGSSEAAAK 14,545 SFV3L_P27401_2mut EAAAKGGSGGG 14,546 FOAMV_P14350_2mut GGSGGS 14,547 FLV_P10273_3mut EAAAKGGG 14,548 FFV_093209-Pro GSSGSSGSSGSSGSS 14,549 SFV3L_P27401 GSSGGGPAP 14,550 PERV_Q4VFZ2_3mutA_WS PAPGGSEAAAK 14,551 SFV3L_P27401-Pro_2mutA GGSPAP 14,552 KORV_Q9TTC1 EAAAKPAPGSS 14,553 KORV_Q9TTC1_3mutA SGSETPGTSESATPES 14,554 SFV1_P23074 GSSPAP 14,555 SFV3L_P27401-Pro_2mutA GSSPAPGGG 14,556 SFV3L_P27401_2mut GGGEAAAKGSS 14,557 SFV1_P23074_2mut GGGPAPGGS 14,558 BAEVM_P10272_3mut EAAAKGGG 14,559 KORV_Q9TTC1-Pro_3mutA GSSGGG 14,560 SFV3L_P27401-Pro_2mut GGSPAPEAAAK 14,561 BAEVM_P10272_3mut EAAAKGSSPAP 14,562 FFV_093209 EAAAKGGGGSEAAAK 14,563 SFV3L_P27401-Pro_2mutA GSSGSSGSSGSSGSS 14,564 SFV1_P23074_2mut EAAAKGGSPAP 14,565 FOAMV_P14350_2mut GGSGGS 14,566 KORV_Q9TTC1-Pro_3mutA EAAAKGSSGGS 14,567 GALV_P21414 GSSGGGPAP 14,568 MLVAV_P03356 PAPEAAAKGGS 14,569 FOAMV_P14350_2mut EAAAKPAPGGG 14,570 AVIRE_P03360_3mut GGSPAP 14,571 SFV3L_P27401_2mutA GGGGSGGGGS 14,572 SFV3L_P27401_2mutA GGGGSS 14,573 AVIRE_P03360_3mutA GGSPAPGGG 14,574 SFV3L_P27401-Pro_2mutA EAAAKPAPGSS 14,575 SFV3L_P27401 EAAAKPAP 14,576 FOAMV_P14350-Pro_2mut PAPEAAAKGSS 14,577 PERV_Q4VFZ2_3mutA_WS EAAAKGGSGSS 14,578 SFV3L_P27401_2mutA GGGEAAAKGSS 14,579 GALV_P21414_3mutA GGGGSEAAAKGGGGS 14,580 PERV_Q4VFZ2_3mut PAPGGSGSS 14,581 FFV_093209-Pro_2mutA GGSEAAAKPAP 14,582 GALV_P21414_3mutA GGSGGSGGSGGSGGS 14,583 FFV_093209-Pro GSSGGSEAAAK 14,584 SFV3L_P27401-Pro_2mut GGS GALV_P21414_3mutA PAPGGSEAAAK 14,586 MLVMS_P03355 PAPEAAAKGGS 14,587 BAEVM_P10272_3mutA GGSGSSPAP 14,588 SFV3L_P27401-Pro_2mutA GSSPAP 14,589 WMSV_P03359_3mut GGGEAAAK 14,590 MMTVB_P03365 GGGGSS 14,591 PERV_Q4VFZ2_3mut GGSPAPGSS 14,592 SFV3L_P27401-Pro_2mut PAPGGS 14,593 MLVBM_Q7SVK7_3mut EAAAKGSSPAP 14,594 MLVBM_Q7SVK7_3mut GGGGSSGGS 14,595 PERV_Q4VFZ2_3mut PAPAPAPAPAPAP 14,596 SFV1_P23074 GGSEAAAKGGG 14,597 SFV3L_P27401-Pro_2mut GGSGGS 14,598 SFV1_P23074_2mut GSSGGGGGS 14,599 MLVF5_P26810_3mutA EAAAKGGGPAP 14,600 SFV3L_P27401 EAAAKEAAAKEAAAKEAAAK 14,601 FOAMV_P14350-Pro_2mutA GGGPAPGSS 14,602 SFV3L_P27401_2mutA GGGGSGGGGSGGGGSGGGGS 14,603 SFV3L_P27401_2mut EAAAKEAAAKEAAAKEAAAK 14,604 MMTVB_P03365_WS PAPGSSGGS 14,605 KORV_Q9TTC1-Pro_3mutA PAPGSSEAAAK 14,606 FOAMV_P14350-Pro_2mut GSSPAPEAAAK 14,607 BAEVM_P10272_3mut EAAAKGGGGSEAAAK 14,608 FFV_093209-Pro GGSPAP 14,609 PERV_Q4VFZ2 GGSGSSEAAAK 14,610 XMRV6_A1Z651_3mut GGSEAAAKGGG 14,611 GALV_P21414_3mutA PAPGGGGSS 14,612 AVIRE_P03360_3mutA GGSGGSGGSGGS 14,613 PERV_Q4VFZ2 GGGGSSGGS 14,614 PERV_Q4VFZ2_3mutA_WS SGGSSGGSSGSETPGTSESATPESSGGSSGGSS 14,615 BAEVM_P10272_3mutA GGGPAP 14,616 MLVAV_P03356_3mut GGGGSGGGGSGGGGSGGGGS 14,617 FFV_093209_2mut GSSEAAAK 14,618 FFV_093209 GGSPAPEAAAK 14,619 FOAMV_P14350_2mut GGGGGSEAAAK 14,620 FOAMV_P14350_2mut GSSPAPGGS 14,621 MLVBM_Q7SVK7_3mut GSS SFVCP_Q87040_2mut EAAAKPAP 14,623 FOAMV_P14350-Pro EAAAKGGG 14,624 SFV3L_P27401_2mut GGGEAAAK 14,625 AVIRE_P03360_3mutA PAPGSSGGG 14,626 WMSV_P03359_3mut EAAAKGGSPAP 14,627 SFV3L_P27401 GSSGGSGGG 14,628 SFV3L_P27401-Pro_2mutA GSSGGGEAAAK 14,629 GALV_P21414_3mutA GGGPAPGSS 14,630 MLVBM_Q7SVK7_3mutA_WS PAPGGGEAAAK 14,631 FFV_093209-Pro_2mut GSSGSSGSSGSS 14,632 SFV1_P23074_2mut GGSEAAAK 14,633 PERV_Q4VFZ2_3mutA_WS GGGEAAAKPAP 14,634 SFV3L_P27401_2mut EAAAKGGGPAP 14,635 SFV3L_P27401_2mut GGGGSSPAP 14,636 FLV_P10273_3mut EAAAKPAPGSS 14,637 FFV_093209_2mut GGGGSSPAP 14,638 SFV3L_P27401_2mut GSSGSS 14,639 KORV_Q9TTC1_3mutA GGGGSGGGGSGGGGSGGGGSGGGGS 14,640 BLVJ_P03361_2mut GGGGSSGGS 14,641 GALV_P21414_3mutA EAAAKGGSGSS 14,642 FFV_093209-Pro EAAAKPAP 14,643 PERV_Q4VFZ2 GSSGGGEAAAK 14,644 MLVBM_Q7SVK7_3mut PAPGGSGGG 14,645 BAEVM_P10272 EAAAKGGGPAP 14,646 MLVF5_P26810 GSSGSSGSS 14,647 MLVBM_Q7SVK7_3mut GSSGGS 14,648 AVIRE_P03360_3mutA GGSEAAAKGGG 14,649 FOAMV_P14350_2mut EAAAKGGS 14,650 MLVF5_P26810_3mutA GGSGSSGGG 14,651 WMSV_P03359_3mut EAAAK 14,652 SFV1_P23074_2mut GSSGGSPAP 14,653 SFV3L_P27401-Pro_2mutA GGGGSSGGS 14,654 KORV_Q9TTC1_3mut PAPGGSGGG 14,655 FFV_093209-Pro_2mut GGGPAPGGS 14,656 SFV3L_P27401_2mutA GSSPAPEAAAK 14,657 FLV_P10273_3mut GGSGSSPAP 14,658 SFV3L_P27401_2mut GSSEAAAKGGS 14,659 SFV3L_P27401_2mut PAPGGG 14,660 SFV3L_P27401_2mutA SGSETPGTSESATPES 14,661 KORV_Q9TTC1-Pro_3mut GGGGS 14,662 SFV1_P23074-Pro_2mutA GSSGGGEAAAK 14,663 WMSV_P03359 EAAAKGGGGSEAAAK 14,664 MLVF5_P26810_3mutA GSSEAAAKPAP 14,665 FFV_093209 GGGGGG 14,666 SFV1_P23074_2mutA EAAAKEAAAKEAAAK 14,667 MMTVB_P03365-Pro EAAAKPAPGSS 14,668 MLVBM_Q7SVK7_3mut GGSGSSEAAAK 14,669 SFV3L_P27401_2mutA GGSEAAAK 14,670 MLVMS_P03355_3mut GGSPAPEAAAK 14,671 SFV3L_P27401_2mut GGGPAPGSS 14,672 SFV1_P23074 GGGGGSEAAAK 14,673 MLVBM_Q7SVK7_3mutA_WS EAAAKPAPGSS 14,674 KORV_Q9TTC1-Pro GSSGSSGSSGSS 14,675 SFV3L_P27401_2mut EAAAKPAP 14,676 SFV3L_P27401_2mut GGGEAAAK 14,677 PERV_Q4VFZ2_3mut GGSGGS 14,678 SFV3L_P27401_2mutA EAAAKGSSGGS 14,679 MMTVB_P03365 SGSETPGTSESATPES 14,680 SFV3L_P27401 EAAAKGSSGGG 14,681 PERV_Q4VFZ2 EAAAKEAAAKEAAAKEAAAKEAAAKEAAAK 14,682 MMTVB_P03365 GGSGGGPAP 14,683 KORV_Q9TTC1_3mutA PAPAPAPAP 14,684 SFV3L_P27401 GGGEAAAKGGS 14,685 SFV1_P23074_2mut GSSGGSGGG 14,686 PERV_Q4VFZ2_3mut PAPEAAAKGGS 14,687 FOAMV_P14350_2mutA GGGEAAAKGSS 14,688 SFV3L_P27401_2mut GGGGSGGGGGGGGSGGGGS 14,689 MLVBM_Q7SVK7 PAPGSSGGG 14,690 FLV_P10273 GGSGSSGGG 14,691 FFV_093209 EAAAKPAPGSS 14,692 MLVBM_Q7SVK7 GSSEAAAKGGG 14,693 SFV3L_P27401_2mutA GGSGGSGGSGGSGGS 14,694 MLVF5_P26810 GGSEAAAKPAP 14,695 SFV3L_P27401-Pro_2mutA EAAAKGGSPAP 14,696 SFV3L_P27401_2mutA EAAAKGGGGGS 14,697 SFV3L_P27401_2mut GSSPAPEAAAK 14,698 SFV3L_P27401_2mutA PAPAP 14,699 MLVBM_Q7SVK7_3mut PAPGGSEAAAK 14,700 KORV_Q9TTC1-Pro GGSGSS 14,701 MLVF5_P26810_3mutA GGSEAAAKPAP 14,702 FFV_093209_2mut GSS MLVMS_P03355 SGGSSGGSSGSETPGTSESATPESSGGSSGGSS 14,704 SFV3L_P27401-Pro PAPGGGEAAAK 14,705 SFV3L_P27401_2mut PAPGGGGGS 14,706 SFV3L_P27401-Pro_2mut PAPGGSGSS 14,707 BAEVM_P10272_3mut GSSGGGEAAAK 14,708 FFV_093209 GGSEAAAKPAP 14,709 SFV1_P23074_2mut GGGGG 14,710 FLV_P10273_3mut GGGEAAAKGSS 14,711 SFV3L_P27401 GSSGSSGSSGSSGSS 14,712 SFV1_P23074-Pro SGSETPGTSESATPES 14,713 AVIRE_P03360 PAPGSSGGG 14,714 MLVBM_Q7SVK7_3mut GGGGSSPAP 14,715 HTL3P_Q4U0X6_2mut GGGEAAAK 14,716 SFV1_P23074 GGSGGG 14,717 AVIRE_P03360 EAAAKGSSGGG 14,718 SFV3L_P27401_2mutA GSSPAPEAAAK 14,719 FOAMV_P14350-Pro_2mutA GGGPAPGSS 14,720 WMSV_P03359 EAAAKGSSGGG 14,721 MLVMS_P03355 GGGGGSEAAAK 14,722 MLVMS_P03355 EAAAKPAPGGS 14,723 SFV3L_P27401 EAAAKGSSPAP 14,724 SFV3L_P27401 GGGGGGG 14,725 FOAMV_P14350_2mutA EAAAKEAAAKEAAAK 14,726 SFV3L_P27401 GSSPAPGGS 14,727 FFV_093209_2mutA GGGGSSEAAAK 14,728 SFV3L_P27401-Pro_2mutA GGSEAAAKGSS 14,729 GALV_P21414_3mutA GGSEAAAKGSS 14,730 BAEVM_P10272_3mutA EAAAKPAPGGG 14,731 MLVCB_P08361 GSSGSSGSSGSSGSSGSS 14,732 SFV1_P23074-Pro GGGGSEAAAKGGGGS 14,733 FOAMV_P14350_2mut GSSPAPGGS 14,734 MLVMS_P03355_PLV919 GGGGSGGGGS 14,735 FFV_093209-Pro GSSGGSPAP 14,736 KORV_Q9TTC1_3mutA GGSGGS 14,737 GALV_P21414_3mutA PAPGSSEAAAK 14,738 WMSV_P03359 PAPGGGGSS 14,739 MMTVB_P03365-Pro GGGGSSGGS 14,740 PERV_Q4VFZ2_3mutA_WS GGGGSGGGGS 14,741 FFV_093209_2mut GGGGSGGGGSGGGGSGGGGS 14,742 XMRV6_A1Z651 GGSGSSEAAAK 14,743 SFV1_P23074_2mut GGSGGGGSS 14,744 GALV_P21414_3mutA GGSEAAAKPAP 14,745 MLVBM_Q7SVK7 EAAAKGGSPAP 14,746 SFV1_P23074_2mutA PAPAPAPAP 14,747 FFV_093209 GSSGGSPAP 14,748 MMTVB_P03365-Pro GGGGGSPAP 14,749 KORV_Q9TTC1_3mutA EAAAKGGGPAP 14,750 PERV_Q4VFZ2 GSSGGSPAP 14,751 BAEVM_P10272 GGGGG 14,752 FFV_093209 GGGGGS 14,753 FLV_P10273_3mutA EAAAKEAAAKEAAAK 14,754 FOAMV_P14350 PAPGGG 14,755 MLVCB_P08361_3mut GSSGGSEAAAK 14,756 FOAMV_P14350_2mutA GGSPAPGGG 14,757 FLV_P10273_3mut GSSGSSGSSGSSGSSGSS 14,758 SFV1_P23074-Pro_2mutA GGSPAPEAAAK 14,759 SFV3L_P27401 PAPGGGGSS 14,760 HTL3P_Q4U0X6_2mutB GGGGSSEAAAK 14,761 MMTVB_P03365_2mut_WS PAPGGS 14,762 MLVRD_P11227_3mut GGSGGSGGSGGSGGS 14,763 MMTVB_P03365 GSAGSAAGSGEF 14,764 AVIRE_P03360 GSSGGS 14,765 BAEVM_P10272_3mutA GGSGGGGSS 14,766 MMTVB_P03365 GGSGGGGSS 14,767 WMSV_P03359 PAPEAAAKGSS 14,768 SFV1_P23074 GSSGSSGSSGSS 14,769 SFV1_P23074-Pro_2mutA PAPAPAPAPAPAP 14,770 SFV3L_P27401 PAPGSSGGG 14,771 FLV_P10273_3mut GGSGSSPAP 14,772 MLVMS_P03355 GGSGGGPAP 14,773 FOAMV_P14350 PAPGGGGGS 14,774 KORV_Q9TTC1_3mutA EAAAKGSSPAP 14,775 GALV_P21414_3mutA GGSGSSPAP 14,776 MLVBM_Q7SVK7_3mut EAAAKGSS 14,777 SFV3L_P27401_2mut GGGGGSEAAAK 14,778 WMSV_P03359 GGGGGGGG 14,779 SFV1_P23074-Pro EAAAKEAAAK 14,780 MLVBM_Q7SVK7 GGGEAAAKGGS 14,781 MLVBM_Q7SVK7 EAAAKGGSPAP 14,782 SFV3L_P27401_2mut GSSEAAAK 14,783 XMRV6_A1Z651 PAPGGGEAAAK 14,784 MMTVB_P03365_WS GGSPAP 14,785 GALV_P21414_3mutA GSSPAPGGG 14,786 MLVBM_Q7SVK7_3mutA_WS GGSGSSPAP 14,787 SFV1_P23074_2mutA GGS HTL32_Q0R5R2_2mut GGSGGGGSS 14,789 MMTVB_P03365-Pro GGGGSGGGGSGGGGSGGGGS 14,790 SFVCP_Q87040_2mutA EAAAKGGGPAP 14,791 FOAMV_P14350_2mut GSSGGGEAAAK 14,792 MMTVB_P03365 SGGSSGGSSGSETPGTSESATPESSGGSSGGSS 14,793 MLVBM_Q7SVK7_3mutA_WS AEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKEAAAKA 14,794 MMTVB_P03365_WS EAAAKEAAAK 14,795 FOAMV_P14350-Pro_2mut GSSPAPEAAAK 14,796 FOAMV_P14350_2mutA EAAAKPAPGGS 14,797 GALV_P21414_3mutA GSSGGSPAP 14,798 KORV_Q9TTC1-Pro_3mut GGGPAPEAAAK 14,799 MLVAV_P03356 GGGEAAAKPAP 14,800 SFV1_P23074-Pro_2mut GGGGGSEAAAK 14,801 SFV3L_P27401_2mut GGGPAPGSS 14,802 SFV3L_P27401_2mut GGSEAAAKPAP 14,803 AVIRE_P03360 GSSGSSGSSGSSGSSGSS 14,804 SFV1_P23074-Pro_2mut EAAAKGSSGGS 14,805 FOAMV_P14350_2mutA GGGGGG 14,806 MLVBM_Q7SVK7_3mut GSSPAPGGS 14,807 PERV_Q4VFZ2 GGSGSSPAP 14,808 GALV_P21414_3mutA GGGPAPEAAAK 14,809 SFV3L_P27401 GGSGGGEAAAK 14,810 WMSV_P03359 GSAGSAAGSGEF 14,811 SFV1_P23074_2mut GSSGGGEAAAK 14,812 MLVMS_P03355 GGG MMTVB_P03365-Pro PAPGSSGGS 14,814 FOAMV_P14350_2mut GGGGSSPAP 14,815 FFV_093209_2mut SGGSSGGSSGSETPGTSESATPESSGGSSGGSS 14,816 MMTVB_P03365_WS GGGGGGG 14,817 XMRV6_A1Z651 PAPAPAPAPAP 14,818 FOAMV_P14350 GGGGSGGGGSGGGGSGGGGS 14,819 MMTVB_P03365_2mut_WS GGSGGGPAP 14,820 SFV3L_P27401_2mut GGGGGG 14,821 SFV1_P23074-Pro EAAAKPAPGSS 14,822 SFV3L_P27401_2mut GGGGSSGGS 14,823 HTL3P_Q4U0X6_2mut PAPGSSEAAAK 14,824 MMTVB_P03365-Pro GGGGSSPAP 14,825 FOAMV_P14350-Pro_2mut PAPGSSGGS 14,826 MMTVB_P03365 AEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKEAAAKA 14,827 SRV2_P51517 PAPAPAP 14,828 MMTVB_P03365_2mut_WS PAPGGGGGS 14,829 MMTVB_P03365_2mutB GGGGSS 14,830 SFV1_P23074-Pro_2mutA EAAAKEAAAKEAAAKEAAAK 14,831 SFV3L_P27401-Pro GGSGGSGGSGGSGGS 14,832 MMTVB_P03365-Pro GGGGGGG 14,833 SFV3L_P27401_2mut PAPGGGEAAAK 14,834 SFV3L_P27401 PAPGSS 14,835 FOAMV_P14350_2mutA GGGGSGGGGS 14,836 SFVCP_Q87040_2mutA GSSGGSGGG 14,837 XMRV6_A1Z651 GGGGSGGGGSGGGGSGGGGSGGGGSGGGGS 14,838 MLVBM_Q7SVK7 GSSEAAAKGGG 14,839 FFV_093209-Pro_2mut GGSEAAAKPAP 14,840 SFV3L_P27401-Pro GSSGGSGGG 14,841 SFV1_P23074_2mut EAAAKGGGGSS 14,842 FOAMV_P14350_2mutA GGGGGG 14,843 SFV3L_P27401_2mut GGGGG 14,844 MLVBM_Q7SVK7_3mut PAPEAAAKGGG 14,845 SFV3L_P27401 EAAAKGGSPAP 14,846 KORV_Q9TTC1_3mutA GGGEAAAKPAP 14,847 SFV1_P23074_2mut GSSGSSGSSGSSGSSGSS 14,848 KORV_Q9TTC1-Pro EAAAKEAAAKEAAAKEAAAK 14,849 SFVCP_Q87040 PAPGSSEAAAK 14,850 MLVBM_Q7SVK7 GSSGSSGSS 14,851 FFV_093209-Pro_2mut GSSGGGPAP 14,852 SFV3L_P27401-Pro_2mut GGGPAPEAAAK 14,853 WMSV_P03359_3mut GGGEAAAK 14,854 MMTVB_P03365-Pro GSSGSSGSSGSS 14,855 SFV3L_P27401-Pro_2mutA PAPAPAPAPAP 14,856 FFV_093209-Pro GGSPAPEAAAK 14,857 FFV_093209-Pro_2mut GSSGSSGSSGSSGSSGSS 14,858 GALV_P21414 EAAAKEAAAKEAAAKEAAAKEAAAK 14,859 FOAMV_P14350 GGGPAPEAAAK 14,860 MMTVB_P03365-Pro PAPGGSGGG 14,861 MLVF5_P26810_3mutA PAPGGSGGG 14,862 FLV_P10273_3mut GGGEAAAKGGS 14,863 SFV3L_P27401 GSAGSAAGSGEF 14,864 MLVBM_Q7SVK7_3mut GSSPAPGGG 14,865 MPMV_P07572_2mutB GSSGSSGSSGSSGSSGSS 14,866 FOAMV_P14350 GGSGGGGSS 14,867 BLVJ_P03361_2mut PAPEAAAKGSS 14,868 SFV1_P23074-Pro GGG FFV_093209 EAAAKGGGGSS 14,870 SFV1_P23074_2mut EAAAKEAAAKEAAAKEAAAKEAAAKEAAAK 14,871 SRV2_P51517 GGGGSGGGGSGGGGSGGGGSGGGGSGGGGS 14,872 MMTVB_P03365 GGGEAAAKGGS 14,873 MMTVB_P03365_WS GSSGSS 14,874 SFV1_P23074 GSSGGGGGS 14,875 SFV3L_P27401 GGGGSSEAAAK 14,876 SFV1_P23074 EAAAKGSSGGS 14,877 HTL1A_P03362_2mutB GSSEAAAKGGS 14,878 GALV_P21414_3mutA EAAAKGSSPAP 14,879 SFV1_P23074 EAAAKPAPGSS 14,880 SFV3L_P27401_2mutA PAPGSSGGG 14,881 SFV3L_P27401-Pro_2mut GGGGSGGGGSGGGGSGGGGSGGGGSGGGGS 14,882 SFV3L_P27401-Pro EAAAKEAAAKEAAAKEAAAKEAAAK 14,883 MMTVB_P03365_WS GGGGSSEAAAK 14,884 MLVF5_P26810_3mutA EAAAKGGSPAP 14,885 GALV_P21414 PAPEAAAKGSS 14,886 MMTVB_P03365_WS GSSGGGGGS 14,887 SFVCP_Q87040_2mut GGGGSSPAP 14,888 SFV1_P23074 EAAAKGGGGSS 14,889 XMRV6_A1Z651 PAPAPAPAP 14,890 MMTVB_P03365 GGSEAAAKGSS 14,891 SFV3L_P27401_2mutA GSSPAPGGG 14,892 MMTVB_P03365_WS GGGGGG 14,893 SFV3L_P27401-Pro GGSGGSGGS 14,894 FOAMV_P14350-Pro_2mut PAPAPAPAPAPAP 14,895 WMSV_P03359 GSSPAP 14,896 MLVBM_Q7SVK7 GGGGGSGSS 14,897 MMTVB_P03365_2mut_WS EAAAKGSSGGS 14,898 MMTVB_P03365_2mutB_WS EAAAK 14,899 FFV_093209_2mutA PAPEAAAK 14,900 SFV1_P23074-Pro EAAAKGGSGSS 14,901 SFV3L_P27401 GGSGGSGGS 14,902 FFV_093209-Pro GSSGGGEAAAK 14,903 MMTVB_P03365 SGGSSGGSSGSETPGTSESATPESSGGSSGGSS 14,904 MLVFF_P26809_3mutA GGSGGSGGSGGSGGSGGS 14,905 HTL1L_POC211_2mutB GGGEAAAK 14,906 SFV3L_P27401-Pro_2mutA GGGGGSGSS 14,907 MMTVB_P03365 GSSPAPGGS 14,908 FOAMV_P14350_2mutA EAAAKGSS 14,909 MLVMS_P03355 GSSGGSGGG 14,910 FFV_093209-Pro GGSGGGGSS 14,911 MMTVB_P03365-Pro_2mut GGSPAPGSS 14,912 FOAMV_P14350_2mut GGSGGSGGSGGSGGSGGS 14,913 SFVCP_Q87040-Pro_2mut GSSEAAAKGGG 14,914 FOAMV_P14350_2mutA GGSGGSGGS 14,915 MMTVB_P03365-Pro GSSGSSGSSGSSGSSGSS 14,916 MMTVB_P03365_2mut_WS GSSGSSGSSGSSGSS 14,917 MMTVB_P03365-Pro PAPEAAAK 14,918 WDSV_092815 GSSGSSGSSGSSGSS 14,919 FFV_093209-Pro_2mut EAAAKGGGGSEAAAK 14,920 MMTVB_P03365-Pro GGSPAPEAAAK 14,921 FOAMV_P14350 GSSGSS 14,922 PERV_Q4VFZ2 GGG MMTVB_P03365-Pro GGGGSGGGGSGGGGS 14,924 FFV_093209_2mut EAAAKEAAAKEAAAKEAAAKEAAAKEAAAK 14,925 MMTVB_P03365-Pro GGSGSSPAP 14,926 WMSV_P03359 GGGGGGGG 14,927 SFV3L_P27401_2mut PAPGSSEAAAK 14,928 FOAMV_P14350-Pro_2mutA GGGGSSPAP 14,929 FOAMV_P14350_2mut GSSGGSPAP 14,930 MLVBM_Q7SVK7_3mut GSSGGGGGS 14,931 GALV_P21414_3mutA EAAAKEAAAKEAAAKEAAAKEAAAK 14,932 MMTVB_P03365 GSSGGGGGS 14,933 SFV1_P23074_2mut GGGGSEAAAKGGGGS 14,934 SFV1_P23074 GGGEAAAKPAP 14,935 FFV_093209 PAPGGGEAAAK 14,936 SFV1_P23074 GGSGGGEAAAK 14,937 PERV_Q4VFZ2_3mutA_WS GSSGGG 14,938 MMTVB_P03365-Pro EAAAKGSSGGS 14,939 FFV_093209_2mut GGGGG 14,940 SFV1_P23074_2mut GGGPAP 14,941 SFV3L_P27401 GSSGGSEAAAK 14,942 FFV_093209 SGGSSGGSSGSETPGTSESATPESSGGSSGGSS 14,943 MMTVB_P03365-Pro GSSGGGEAAAK 14,944 SFV1_P23074_2mutA GSSGSSGSSGSSGSS 14,945 SFV3L_P27401_2mut GGSEAAAKPAP 14,946 FLV_P10273 GGGGSGGGGS 14,947 FOAMV_P14350-Pro_2mutA GSSEAAAKPAP 14,948 SFV3L_P27401 GGGGSEAAAKGGGGS 14,949 MMTVB_P03365-Pro PAPGSSEAAAK 14,950 MLVF5_P26810_3mut EAAAKGGSGGG 14,951 SFV3L_P27401 GGGPAPGGS 14,952 SFV3L_P27401 GSSEAAAKGGS 14,953 FOAMV_P14350_2mutA EAAAKGGSGGG 14,954 HTL1L_POC211 GSSGGSPAP 14,955 SFV3L_P27401_2mutA PAPAP 14,956 FFV_093209 PAPGGSGSS 14,957 MMTVB_P03365_WS EAAAKGGGGGS 14,958 FOAMV_P14350_2mut PAPEAAAKGGS 14,959 SFV3L_P27401_2mut GSSEAAAKPAP 14,960 MMTVB_P03365-Pro GGSGGS 14,961 PERV_Q4VFZ2_3mut GSSEAAAKGGG 14,962 FFV_093209-Pro_2mutA EAAAK 14,963 HTL1L_POC211 GSSPAP 14,964 MLVMS_P03355 EAAAKPAPGGG 14,965 FFV_093209-Pro_2mut GGGGSEAAAKGGGGS 14,966 SFV1_P23074-Pro_2mut EAAAKGSSGGS 14,967 SFV3L_P27401 GSAGSAAGSGEF 14,968 FFV_093209_2mutA PAPEAAAKGGS 14,969 MMTVB_P03365_2mutB_WS EAAAKEAAAKEAAAKEAAAKEAAAKEAAAK 14,970 MMTVB_P03365 GGS MMTVB_P03365 GGSEAAAKPAP 14,972 SFV1_P23074 EAAAKGSSGGG 14,973 HTLV2_P03363_2mut GGSEAAAKGGG 14,974 MMTVB_P03365_WS GGSGGS 14,975 FFV_093209-Pro GSSEAAAKGGS 14,976 MMTVB_P03365-Pro PAPAPAPAPAP 14,977 SFV1_P23074_2mutA GGSEAAAKGGG 14,978 MMTVB_P03365_2mutB_WS PAPAPAPAP 14,979 MMTVB_P03365_WS GGGGSGGGGSGGGGSGGGGSGGGGS 14,980 HTL3P_Q4U0X6_2mut PAPGGSEAAAK 14,981 SFV1_P23074-Pro_2mut GGSGGGPAP 14,982 MMTVB_P03365 GSSGSSGSSGSSGSSGSS 14,983 MMTVB_P03365-Pro GGSEAAAKPAP 14,984 SFV1_P23074-Pro GGGEAAAKGSS 14,985 SFV3L_P27401_2mutA GGGPAPGGS 14,986 AVIRE_P03360 PAPGGG 14,987 MLVRD_P11227 GGSEAAAKGSS 14,988 SFV3L_P27401_2mut GGGEAAAKGSS 14,989 FOAMV_P14350_2mut GGGEAAAKGSS 14,990 SFV1_P23074-Pro EAAAKEAAAKEAAAKEAAAK 14,991 MLVAV_P03356 EAAAKGGGPAP 14,992 JSRV_P31623_2mutB EAAAKGGGGSS 14,993 FOAMV_P14350_2mut EAAAKEAAAKEAAAKEAAAKEAAAK 14,994 SRV2_P51517 GSSGGGGGS 14,995 FFV_093209 PAPAPAP 14,996 FOAMV_P14350_2mutA GGSGGSGGSGGS 14,997 FOAMV_P14350 GGGEAAAK 14,998 MMTVB_P03365_WS GGGGGS 14,999 SFV1_P23074_2mutA GGSGGS 15,000 WMSV_P03359_3mut EAAAKGGS 15,001 MMTVB_P03365-Pro GGGGSS 15,002 BLVJ_P03361_2mut PAPAP 15,003 MMTVB_P03365-Pro_2mut PAPGGG 15,004 SMRVH_P03364 EAAAKGGGGSS 15,005 SFV3L_P27401 PAPAPAPAPAP 15,006 MMTVB_P03365 GGGPAP 15,007 MMTVB_P03365-Pro GSSGGSGGG 15,008 MMTVB_P03365 EAAAKGGGPAP 15,009 FOAMV_P14350_2mutA GSSGSSGSSGSS 15,010 SFV1_P23074 GGGGSGGGGS 15,011 SFV3L_P27401 GSSGGSGGG 15,012 MLVF5_P26810 GGGEAAAKPAP 15,013 MMTVB_P03365-Pro PAPEAAAK 15,014 HTLV2_P03363_2mut GSSGSSGSSGSS 15,015 FOAMV_P14350_2mut GSSEAAAKPAP 15,016 MMTVB_P03365-Pro PAPEAAAKGGG 15,017 HTL3P_Q4U0X6_2mut GGSEAAAKGSS 15,018 MMTVB_P03365-Pro EAAAKPAPGGS 15,019 MMTVB_P03365_2mut_WS GSSGGSEAAAK 15,020 MLVF5_P26810_3mutA GGGGSGGGGSGGGGGGGGSGGGGSGGGGS 15,021 MLVF5_P26810_3mut EAAAKGGGGSS 15,022 MMTVB_P03365-Pro GGGGGSGSS 15,023 HTL1A_P03362_2mutB PAPAP 15,024 FFV_093209-Pro_2mut GGGGGSPAP 15,025 HTL1C_P14078_2mut GGGPAP 15,026 HTLV2_P03363_2mut EAAAKGGGGSEAAAK 15,027 SFVCP_Q87040 GGSEAAAKGGG 15,028 FFV_093209-Pro_2mutA GSSPAPGGS 15,029 FOAMV_P14350-Pro_2mut GGGGGGG 15,030 MMTVB_P03365-Pro EAAAKGSS 15,031 SFV3L_P27401_2mutA EAAAKGGGGSEAAAK 15,032 MMTVB_P03365-Pro GGGGSEAAAKGGGGS 15,033 SFV1_P23074-Pro_2mutA EAAAKGGGGSS 15,034 MMTVB_P03365 GGGEAAAKGGS 15,035 SFV1_P23074 PAPEAAAKGGG 15,036 MLVF5_P26810 GGGGSSGGS 15,037 MMTVB_P03365 GGSGSS 15,038 MMTVB_P03365 PAPAPAPAPAPAP 15,039 KORV_Q9TTC1 EAAAKGGG 15,040 SFV1_P23074-Pro_2mut PAPAPAPAPAPAP 15,041 SRV2_P51517 GSSGSSGSSGSSGSS 15,042 FFV_093209-Pro_2mutA GGGGSS 15,043 FOAMV_P14350_2mut PAPGGGEAAAK 15,044 MMTVB_P03365_WS GGSGGGEAAAK 15,045 FFV_093209-Pro_2mut PAPAPAPAPAP 15,046 MMTVB_P03365_WS GGGEAAAKGGS 15,047 MMTVB_P03365-Pro GGGEAAAKGSS 15,048 MMTVB_P03365_2mutB GSSPAPEAAAK 15,049 MMTVB_P03365_WS EAAAKEAAAKEAAAKEAAAKEAAAK 15,050 SFV1_P23074-Pro_2mutA PAPGGG 15,051 SFV3L_P27401 GSSEAAAKGGG 15,052 MMTVB_P03365_WS GGGGSSEAAAK 15,053 FOAMV_P14350_2mut PAPGSSGGS 15,054 SFV1_P23074-Pro_2mut GSSGSSGSSGSSGSSGSS 15,055 SFV3L_P27401 EAAAKGSSGGG 15,056 MMTVB_P03365 PAPGGGGSS 15,057 WDSV_092815_2mutA GGSPAP 15,058 MMTVB_P03365-Pro GGSGGSGGSGGSGGS 15,059 SFVCP_Q87040-Pro_2mut PAPAPAPAP 15,060 MMTVB_P03365-Pro GGGGG 15,061 HTL1A_P03362 GGSGGSGGSGGS 15,062 SFV1_P23074_2mutA GSSGSSGSSGSSGSS 15,063 FOAMV_P14350-Pro_2mut PAPGGSEAAAK 15,064 MMTVB_P03365_2mutB_WS PAPAPAPAP 15,065 SFV1_P23074_2mut PAPGGGGSS 15,066 MMTVB_P03365 GGSGSS 15,067 SFV3L_P27401_2mut EAAAKEAAAKEAAAKEAAAK 15,068 MMTVB_P03365_2mut EAAAKGGSGGG 15,069 HTL3P_Q4U0X6_2mut PAPGGGGSS 15,070 SFVCP_Q87040-Pro_2mutA EAAAKGGGGGS 15,071 MLVAV_P03356 GGGGGS 15,072 FOAMV_P14350_2mut GGGEAAAKGGS 15,073 FFV_093209-Pro_2mutA EAAAKPAPGGG 15,074 MMTVB_P03365_2mutB GGSGGGPAP 15,075 FFV_093209_2mut GSSEAAAKPAP 15,076 MMTVB_P03365 PAPAPAPAPAPAP 15,077 SFV1_P23074_2mut GGSPAPGGG 15,078 MMTVB_P03365-Pro GGSGGGEAAAK 15,079 MMTVB_P03365 PAPAP 15,080 SFVCP_Q87040 GSSEAAAK 15,081 SFVCP_Q87040 GGGGSGGGGSGGGGS 15,082 MMTVB_P03365-Pro GSSGSSGSS 15,083 SFV3L_P27401 EAAAKGGSGGG 15,084 MMTVB_P03365-Pro GSSPAP 15,085 SFV1_P23074_2mut GGGEAAAK 15,086 SFV1_P23074-Pro AEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKEAAAKA 15,087 MMTVB_P03365-Pro PAPGGS 15,088 HTL1C_P14078_2mut PAPGSSGGS 15,089 SFV1_P23074_2mut PAPEAAAK 15,090 MMTVB_P03365_WS PAPAP 15,091 MMTVB_P03365-Pro EAAAKGGS 15,092 HTL1A_P03362_2mut GGGGSEAAAKGGGGS 15,093 HTL1C_P14078 EAAAKGSSGGS 15,094 FOAMV_P14350-Pro PAPGGSGSS 15,095 MMTVB_P03365-Pro PAPGGSEAAAK 15,096 SFV1_P23074_2mut PAPGSSEAAAK 15,097 FFV_093209-Pro_2mut PAPGSSGGG 15,098 FOAMV_P14350-Pro_2mutA GSSGGGEAAAK 15,099 AVIRE_P03360 GGGGGG 15,100 SMRVH_P03364_2mut PAPEAAAKGGG 15,101 MMTVB_P03365-Pro GGGEAAAKGGS 15,102 SFVCP_Q87040_2mutA PAPAPAPAPAP 15,103 SRV2_P51517 GSSGSSGSSGSSGSSGSS 15,104 MMTVB_P03365 EAAAKGGGPAP 15,105 MLVAV_P03356 PAPAPAPAPAP 15,106 FOAMV_P14350-Pro_2mutA PAPGGSEAAAK 15,107 FOAMV_P14350 GSSGGGPAP 15,108 HTL32_Q0R5R2_2mutB GGGGGSPAP 15,109 HTL3P_Q4U0X6_2mutB GSSGGSGGG 15,110 MMTVB_P03365-Pro PAPAP 15,111 SFVCP_Q87040-Pro GSSGGGPAP 15,112 MMTVB_P03365-Pro GGSGSS 15,113 MMTVB_P03365-Pro_2mut GGSPAPEAAAK 15,114 SFV1_P23074-Pro_2mut EAAAKGGSGGG 15,115 SFV3L_P27401_2mut GGGGSSEAAAK 15,116 MMTVB_P03365_WS GGGGGSGSS 15,117 MMTVB_P03365_2mut GGGGSSGGS 15,118 SFV1_P23074-Pro_2mutA EAAAKGGGGSEAAAK 15,119 MMTVB_P03365_WS PAPGGGEAAAK 15,120 SFV1_P23074-Pro PAPEAAAKGGG 15,121 MMTVB_P03365 AEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKEAAAKA 15,122 MMTVB_P03365 GSSGGSEAAAK 15,123 FOAMV_P14350-Pro_2mut GGSPAP 15,124 MLVBM_Q7SVK7_3mut GSSEAAAK 15,125 FOAMV_P14350 GSSEAAAK 15,126 MMTVB_P03365-Pro EAAAKGSSGGS 15,127 HTL1A_P03362_2mut GGGEAAAKPAP 15,128 FOAMV_P14350-Pro_2mut EAAAKGGSPAP 15,129 FOAMV_P14350 GSSEAAAKPAP 15,130 MMTVB_P03365_WS GSSGSSGSS 15,131 FOAMV_P14350_2mut EAAAKEAAAKEAAAKEAAAK 15,132 MMTVB_P03365_WS EAAAK 15,133 MMTVB_P03365 PAPGSS 15,134 BAEVM_P10272 PAPGGS 15,135 FFV_093209-Pro_2mut GGSGGS 15,136 SFV1_P23074-Pro_2mutA SGGSSGGSSGSETPGTSESATPESSGGSSGGSS 15,137 HTLV2_P03363_2mut GGSGGGEAAAK 15,138 MMTVB_P03365_WS PAPGSSGGG 15,139 HTL1A_P03362 GGSGGS 15,140 SFV3L_P27401-Pro GSSGSS 15,141 SFV1_P23074-Pro PAPGGSEAAAK 15,142 MMTVB_P03365 GSAGSAAGSGEF 15,143 MMTVB_P03365-Pro PAPGGG 15,144 FOAMV_P14350_2mut EAAAKGGSGSS 15,145 MMTVB_P03365_WS GSSGGGEAAAK 15,146 SFV3L_P27401-Pro GGSGGGPAP 15,147 FOAMV_P14350-Pro_2mut PAPAPAPAPAPAP 15,148 WDSV_092815 SGSETPGTSESATPES 15,149 SFVCP_Q87040-Pro_2mutA GGSGGSGGS 15,150 SFV1_P23074 GGGGSS 15,151 SFVCP_Q87040_2mut GGGGGSEAAAK 15,152 MMTVB_P03365 SGSETPGTSESATPES 15,153 MMTVB_P03365_WS PAPAPAP 15,154 SFV3L_P27401 PAPEAAAKGSS 15,155 MMTVB_P03365_2mutB_WS GSSGSSGSSGSSGSS 15,156 SRV2_P51517 GGGPAPGSS 15,157 HTL32_Q0R5R2_2mutB GGSGGGGSS 15,158 MMTVB_P03365-Pro SGSETPGTSESATPES 15,159 SRV2_P51517 EAAAKGSSGGS 15,160 MMTVB_P03365-Pro GSSPAPEAAAK 15,161 MMTVB_P03365-Pro GSSPAPEAAAK 15,162 SRV2_P51517 GGGGSSPAP 15,163 MMTVB_P03365-Pro PAPGGGEAAAK 15,164 SFV1_P23074-Pro_2mutA PAPEAAAKGGS 15,165 MMTVB_P03365 GSSGSSGSSGSSGSSGSS 15,166 FOAMV_P14350-Pro GGSPAPGSS 15,167 SFV3L_P27401 GGGPAPGGS 15,168 SFV1_P23074-Pro_2mutA GGGPAPGSS 15,169 MMTVB_P03365-Pro EAAAKPAP 15,170 MLVBM_Q7SVK7 EAAAKEAAAKEAAAK 15,171 HTL1C_P14078 GSSGGSEAAAK 15,172 SRV2_P51517 PAPGGGGGS 15,173 SRV2_P51517 GGGEAAAK 15,174 FFV_093209-Pro_2mut EAAAKGGGPAP 15,175 HTL32_QOR5R2 GGSGSSGGG 15,176 MMTVB_P03365 PAPEAAAKGSS 15,177 MMTVB_P03365-Pro PAPGGGGGS 15,178 MMTVB_P03365-Pro EAAAKGGGGGS 15,179 MMTVB_P03365_WS GGGGGS 15,180 MMTVB_P03365-Pro GGGGSGGGGSGGGGSGGGGSGGGGS 15,181 HTL1C_P14078 EAAAKGGSPAP 15,182 MMTVB_P03365 GGGGSSPAP 15,183 FFV_093209-Pro_2mut GGGGSSGGS 15,184 MMTVB_P03365-Pro PAPGSSGGS 15,185 MMTVB_P03365-Pro GGGGGS 15,186 SRV2_P51517 GGSGSSGGG 15,187 MMTVB_P03365 GSSGGSEAAAK 15,188 MMTVB_P03365-Pro EAAAKEAAAKEAAAKEAAAK 15,189 GALV_P21414 GGSEAAAKGGG 15,190 MMTVB_P03365-Pro SGGSSGGSSGSETPGTSESATPESSGGSSGGSS 15,191 MMTVB_P03365-Pro GSSEAAAKGGS 15,192 MMTVB_P03365 GGGGSGGGGSGGGGSGGGGSGGGGGGGGS 15,193 HTL3P_Q4U0X6_2mutB GGGEAAAK 15,194 MMTVB_P03365-Pro PAPAPAPAP 15,195 MMTVB_P03365-Pro PAPGSSGGG 15,196 MMTVB_P03365 GSSGSSGSSGSSGSS 15,197 GALV_P21414 GGSPAP 15,198 MMTVB_P03365_WS GGGGSGGGGSGGGGSGGGGSGGGGSGGGGS 15,199 MMTVB_P03365-Pro PAPEAAAK 15,200 MMTVB_P03365-Pro PAPGSSGGG 15,201 SFV1_P23074-Pro_2mutA GGGGGSEAAAK 15,202 MMTVB_P03365_2mutB_WS PAPAPAPAPAP 15,203 MMTVB_P03365-Pro EAAAKGGSGSS 15,204 MMTVB_P03365-Pro EAAAKEAAAKEAAAKEAAAK 15,205 MLVRD_P11227_3mut PAPAPAPAP 15,206 FOAMV_P14350_2mutA GGGPAPGSS 15,207 SFVCP_Q87040_2mut PAPEAAAKGSS 15,208 SFVCP_Q87040_2mut GGSPAPGGG 15,209 MMTVB_P03365-Pro GGGGSGGGGSGGGGSGGGGS 15,210 MMTVB_P03365 EAAAKGGS 15,211 HTL3P_Q4U0X6_2mut PAPGSSGGS 15,212 MMTVB_P03365_WS GGGGSGGGGS 15,213 MMTVB_P03365 GGSGGS 15,214 FOAMV_P14350 EAAAKGGGGSEAAAK 15,215 SFVCP_Q87040-Pro_2mut EAAAKEAAAKEAAAKEAAAK 15,216 MMTVB_P03365-Pro_2mutB PAPGGGEAAAK 15,217 SFVCP_Q87040-Pro GSSGSS 15,218 JSRV_P31623_2mutB EAAAKGGGGGS 15,219 MMTVB_P03365_2mut_WS GSSPAPEAAAK 15,220 MMTVB_P03365-Pro GGGEAAAK 15,221 HTL1C_P14078 PAPEAAAKGSS 15,222 HTL32_Q0R5R2_2mutB GGGGSSEAAAK 15,223 MMTVB_P03365-Pro PAPGSSGGS 15,224 MMTVB_P03365-Pro EAAAKGGGGGS 15,225 MMTVB_P03365 GGGGSGGGGSGGGGSGGGGS 15,226 MMTVB_P03365 EAAAKGGGGSS 15,227 HTL3P_Q4U0X6_2mut GGGEAAAKGGS 15,228 SFVCP_Q87040-Pro GGGGGSPAP 15,229 MMTVB_P03365-Pro_2mutB GGSGGGEAAAK 15,230 SFV3L_P27401-Pro PAPGGGGGS 15,231 SFV3L_P27401-Pro EAAAKGGGGSEAAAK 15,232 MMTVB_P03365 PAPEAAAKGSS 15,233 MMTVB_P03365-Pro GGSEAAAKGGG 15,234 MMTVB_P03365-Pro GGSGGSGGSGGSGGS 15,235 SMRVH_P03364_2mutB GGSGGSGGSGGSGGS 15,236 HTL1L_POC211_2mut GGGGGG 15,237 WDSV_092815 GGGGGSGSS 15,238 MMTVB_P03365-Pro GGSEAAAKPAP 15,239 SFV3L_P27401-Pro_2mut GGGPAPGSS 15,240 MMTVB_P03365_2mut_WS GGGGGS 15,241 MMTVB_P03365_WS GGSPAPEAAAK 15,242 MMTVB_P03365 PAPEAAAKGGS 15,243 HTL1A_P03362 EAAAKGGSGSS 15,244 MMTVB_P03365_2mut_WS GGGPAPEAAAK 15,245 SFV3L_P27401-Pro_2mut PAPGGGGSS 15,246 HTL32_Q0R5R2_2mut GSSPAPGGG 15,247 HTL3P_Q4U0X6_2mut GGGGSSGGS 15,248 BLVAU_P25059_2mut EAAAKGGGGGS 15,249 HTL1L_POC211 GGSEAAAKGSS 15,250 JSRV_P31623_2mutB GSSGGG 15,251 JSRV_P31623 GGSGGSGGSGGS 15,252 MMTVB_P03365-Pro EAAAKPAP 15,253 SFV1_P23074-Pro_2mutA GGGGSSGGS 15,254 MMTVB_P03365_WS GGSGGS 15,255 MMTVB_P03365_WS EAAAKGGGGGS 15,256 MMTVB_P03365-Pro GGGGSGGGGSGGGGGGGGSGGGGSGGGGS 15,257 MMTVB_P03365 GGSGGSGGS 15,258 MMTVB_P03365 GGGGGSEAAAK 15,259 MLVBM_Q7SVK7 GGSGSSPAP 15,260 MMTVB_P03365_WS EAAAKEAAAKEAAAK 15,261 JSRV_P31623 PAPEAAAKGGS 15,262 MMTVB_P03365-Pro GGSGSSEAAAK 15,263 FOAMV_P14350 GGGGGSGSS 15,264 MMTVB_P03365-Pro_2mut GGGPAPGGS 15,265 MMTVB_P03365 SGSETPGTSESATPES 15,266 SFVCP_Q87040_2mut GSSPAPGGS 15,267 SFV1_P23074-Pro_2mutA GSSGSSGSSGSSGSS 15,268 MMTVB_P03365 EAAAKGGGPAP 15,269 MMTVB_P03365 GSSGGG 15,270 MMTVB_P03365_2mut_WS GGGEAAAKPAP 15,271 MMTVB_P03365 PAPGGSGGG 15,272 MMTVB_P03365-Pro GSSGGSGGG 15,273 WDSV_092815_2mut GGSGGG 15,274 HTL32_Q0R5R2_2mut EAAAKGGSPAP 15,275 HTLV2_P03363_2mut GGSPAPEAAAK 15,276 MMTVB_P03365-Pro GSSGGSEAAAK 15,277 MMTVB_P03365_2mut GSAGSAAGSGEF 15,278 MMTVB_P03365_WS PAPGGSGSS 15,279 FFV_093209 GGSEAAAKGGG 15,280 MMTVB_P03365 GGSPAPGSS 15,281 MMTVB_P03365-Pro GSSGGSGGG 15,282 SFV3L_P27401 PAPEAAAKGGG 15,283 HTL1A_P03362_2mutB GGGEAAAKPAP 15,284 MMTVB_P03365-Pro GGSEAAAK 15,285 HTL32_QOR5R2_2mutB GGGEAAAKGSS 15,286 MPMV_P07572 GGGGGSEAAAK 15,287 MMTVB_P03365-Pro PAPAPAPAPAP 15,288 SFVCP_Q87040-Pro_2mutA PAPAPAPAPAP 15,289 HTL1L_POC211_2mut GGGGSSGGS 15,290 HTL3P_Q4U0X6 PAPGGSEAAAK 15,291 MMTVB_P03365_2mut_WS PAPAPAPAPAP 15,292 HTL1A_P03362 EAAAKPAPGGG 15,293 MMTVB_P03365_2mut_WS GGSEAAAK 15,294 MMTVB_P03365_2mut_WS GGGEAAAKGSS 15,295 SFV1_P23074-Pro_2mutA GGSPAPGSS 15,296 MMTVB_P03365-Pro GGSEAAAKPAP 15,297 MLVBM_Q7SVK7 PAPEAAAKGGG 15,298 MMTVB_P03365_2mut_WS GSSEAAAKPAP 15,299 MMTVB_P03365-Pro_2mutB GGGGSEAAAKGGGGS 15,300 MMTVB_P03365-Pro_2mut GSSEAAAKGGS 15,301 MMTVB_P03365-Pro_2mutB GSSGSSGSSGSSGSS 15,302 SRV2_P51517_2mutB GGGGGSPAP 15,303 HTL1L_POC211_2mut GGSEAAAK 15,304 MMTVB_P03365 GSSPAPEAAAK 15,305 SMRVH_P03364_2mutB GGGPAPGGS 15,306 HTL1C_P14078_2mut GGSPAPEAAAK 15,307 MMTVB_P03365_WS GGSEAAAKPAP 15,308 HTL1A_P03362_2mut PAPAPAPAP 15,309 HTLV2_P03363_2mut GSSPAPGGG 15,310 MMTVB_P03365 GSSGSSGSSGSS 15,311 MMTVB_P03365-Pro GGSEAAAKGSS 15,312 MMTVB_P03365_WS GGSGSSGGG 15,313 MMTVB_P03365_2mutB GSSGSSGSSGSSGSSGSS 15,314 JSRV_P31623_2mutB GGSEAAAKPAP 15,315 MMTVB_P03365-Pro GSSGGSGGG 15,316 HTLV2_P03363_2mut AEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKEAAAKA 15,317 WDSV_092815_2mut GGSPAPEAAAK 15,318 MMTVB_P03365 GGGGSSEAAAK 15,319 MMTVB_P03365 GGSGGGEAAAK 15,320 SFV1_P23074-Pro_2mutA GGGGSEAAAKGGGGS 15,321 WDSV_092815_2mut GGSGSSEAAAK 15,322 MMTVB_P03365_2mutB_WS GGSEAAAKPAP 15,323 MMTVB_P03365_WS GSSGGGEAAAK 15,324 SFVCP_Q87040-Pro GSSGGS 15,325 SFVCP_Q87040-Pro_2mut GGSEAAAKPAP 15,326 SFVCP_Q87040_2mut GSSGGSEAAAK 15,327 SFVCP_Q87040_2mut GSSPAPEAAAK 15,328 SRV2_P51517_2mutB GGSGGSGGSGGSGGSGGS 15,329 BLVAU_P25059 GSSGSSGSSGSSGSS 15,330 HTL1C_P14078_2mut EAAAKGGGGSS 15,331 MMTVB_P03365_2mutB GGGEAAAKGSS 15,332 SFVCP_Q87040-Pro

Example 3: Sequencing Analysis of Pooled Screening of Gene Modifying Polypeptides in HEK293T and U2OS Cells

This example describes identification and characterization of several classes of gene modifying polypeptides capable of editing genomic DNA.

Genomic DNA was extracted from pools of the sorted and unsorted cell populations in Example 2 and analysed as described in Example 1. Specifically, DNA libraries were prepared by PCR amplification of candidate gene modifying polypeptide sequences. Libraries were sequenced using long read sequencing using an Oxford Nanopore Technologies sequencer protocol Amplicons by Ligation SQK-LSK110. Raw sequencing reads were processed using MinKNOW (Oxford Nanopore Technologies) to perform base-calling and standard quality filtering. The filtered sequencing reads were then mapped against a reference consisting of full-length DNA sequences for all possible library candidates. Following mapping, the data were further processed to remove reads not satisfying requirements for minimum and maximum length, excessive truncation, chimerism, and minimum sequence identity to improve mapping confidence. The surviving data were then normalized to counts-per-million to adjust for sequencing depth. Normalized counts from unsorted populations were used as baseline for their respective sorted populations to calculate fold-change enrichment for each candidate. Finally, fold-change values were log₂ transformed and Z-score normalized.

Cells infected with lentiviral pools encoding gene modifying polypeptides comprising MLVMS RT having high editing activity with several linkers were used as a positive control and cells infected with lentiviral pools encoding gene modifying polypeptides comprising MMTVB RT having low editing activity were used as a negative control to confirm that sequencing analyses were consistent with known editing assay results (FIGS. 4A-4C). The results showed that the assay distinguishes between gene modifying polypeptides containing high activity RTs and low activity RTs (FIGS. 4A-4B). The results further showed that the activity trends associated with the positive control RT and negative control RT selected are consistent across all members of a given RT family tested, e.g., for each of the MLVMS RT sequences and each of the MMTVB RT sequences across multiple linkers tested (FIG. 4C). These data indicate that the identity of the RT domain plays a significant role in determining editing activity of a gene modifying polypeptide.

The genome-editing capacity of gene modifying library candidates tested was assessed across four conditions, using two different templates and two different cell lines: template g4 in HEK293T cells (condition 1), template g4 in U2OS cells (condition 2), template g10 in HEK293T cells (condition 3), and template g10 in U2OS cells (condition 4). Genome editing activity was plotted as log 2 (Fold Change CPM) in a violin plot and the data for candidates were sorted by RT family (FIGS. 5A-5D). The results showed editing activity for gene modifying candidates containing linkers paired with RT sequences from across 17 different retroviral RT families tested in the assay: AVIRE, BAEVM, FFV, FLV, FOAMV, GALV, KORV, MLVAV, MLVBM, MLVCB, MLVFF, MLVMS, PERV, SFV1, SFV3L, WMSV, and XMRV6. In contrast, gene modifying candidates with RT sequences from other RT families tested lacked editing activity or had lower levels of editing activity. Regression analysis showed that editing activity of gene modifying polypeptide candidates was correlated across HEK293T and U2OS conditions (FIG. 6 ), as well as across templates g4 and g10 (FIG. 7 ). The overall activity trends of all candidate gene modifying polypeptides showed that editing activity remained consistent across the four conditions tested, suggesting that gene modifying polypeptide editing activity may translate across different cell types and templates.

Data from the four conditions tested were analyzed to select subsets of gene modifying polypeptide candidates displaying consistent and robust evidence of genome editing activity. Namely, selected candidates were required to exhibit an enrichment Z-score of 1 or higher in one or more of the template g4 conditions in HEK293T and U2OS cells (conditions 1 and 2, respectively) and the test template g10 condition in HEK293T cells (condition 3). Data from the test template g10 condition (condition 4) in U2OS cells were omitted from initial analysis. An exemplary selection analysis is depicted graphically in FIG. 14 which displays gene modifying candidates showing high genome editing activity across both cells types for test template g4 and in HEK293T cells for test template g10 in HEK293T cells.

Approximately 3180 gene modifying polypeptide candidates within the library had a Z-score of at least 1 or greater in any one of conditions 1, 2, or 3. These results show that this subset of gene modifying polypeptides had editing activity in at least one condition of the screening assay (FIG. 14 , light and dark dots). The subset of these gene modifying polypeptides are encoded by amino acid sequences of any one of the SEQ ID NOs listed in Table D1 below.

TABLE D1 Gene modifying polypeptide candidates having a Z-score of at least 1 or greater in any one of conditions 1, 2, or 3. SEQ ID NOs 1 255 631 964 1208 1551 1803 2028 2324 2563 2781 3001 4524 6434 6879 7296 2 256 636 965 1209 1552 1804 2029 2325 2564 2782 3002 4525 6439 6881 7298 3 257 645 966 1210 1553 1805 2030 2326 2565 2783 3003 4526 6442 6882 7299 4 258 647 967 1211 1555 1806 2031 2327 2566 2784 3005 4527 6443 6883 7301 5 259 648 968 1212 1556 1808 2033 2328 2567 2785 3007 4528 6444 6884 7302 6 261 649 969 1213 1557 1809 2034 2329 2568 2786 3008 4529 6445 6885 7305 7 262 650 970 1214 1558 1810 2035 2330 2569 2787 3009 4530 6449 6886 7306 9 263 651 971 1215 1559 1811 2037 2331 2570 2788 3010 4531 6453 6887 7307 10 264 652 972 1216 1561 1813 2038 2332 2571 2789 3011 4532 6454 6890 7311 13 265 653 973 1217 1563 1816 2039 2333 2572 2790 3012 4533 6457 6891 7312 14 268 656 974 1218 1564 1817 2041 2334 2573 2791 3014 4534 6458 6896 7313 17 269 657 975 1219 1565 1818 2042 2335 2574 2792 3015 4535 6462 6897 7314 19 270 659 976 1220 1566 1819 2045 2336 2575 2793 3016 4536 6465 6898 7317 22 271 661 977 1221 1567 1824 2048 2337 2576 2794 3017 4537 6478 6901 7320 33 273 662 978 1222 1568 1825 2049 2338 2577 2795 3018 4538 6479 6902 7322 34 274 663 979 1223 1570 1827 2050 2339 2578 2796 3019 4539 6480 6904 7323 35 278 664 980 1224 1571 1828 2051 2340 2579 2797 3020 4540 6486 6905 7326 36 279 667 981 1225 1572 1829 2052 2341 2580 2798 3021 4541 6488 6907 7328 37 280 668 982 1226 1573 1831 2053 2342 2581 2799 3022 6001 6491 6908 7329 38 281 670 983 1227 1574 1834 2054 2343 2582 2800 3025 6004 6492 6910 7335 39 283 677 984 1228 1576 1838 2055 2344 2583 2801 3026 6007 6495 6911 7336 40 285 679 985 1229 1577 1840 2056 2345 2584 2802 3027 6008 6497 6915 7339 41 290 687 986 1230 1578 1842 2057 2346 2585 2803 3028 6012 6499 6917 7342 42 293 689 987 1231 1579 1843 2058 2347 2586 2804 3030 6013 6501 6919 7343 43 294 690 988 1232 1580 1844 2060 2348 2587 2805 3031 6014 6502 6923 7345 44 295 694 989 1233 1581 1845 2061 2349 2588 2806 3033 6015 6503 6925 7346 45 298 700 990 1234 1582 1846 2062 2350 2589 2807 3034 6021 6505 6928 7347 46 300 707 991 1235 1583 1847 2069 2351 2590 2808 3035 6022 6511 6930 7349 47 302 711 992 1236 1585 1848 2070 2352 2591 2809 3036 6023 6512 6932 7350 48 303 715 993 1237 1588 1849 2071 2353 2592 2810 3037 6024 6515 6933 7352 49 304 716 994 1238 1590 1850 2074 2354 2593 2811 3038 6025 6520 6942 7357 50 305 717 996 1239 1593 1851 2075 2355 2594 2812 3039 6026 6524 6943 7358 51 306 720 997 1240 1594 1852 2076 2356 2595 2813 3040 6028 6525 6951 7360 52 308 726 999 1241 1597 1853 2081 2357 2596 2814 3041 6029 6527 6952 7361 53 309 727 1000 1242 1598 1855 2082 2358 2597 2815 3042 6030 6529 6963 7362 54 310 728 1002 1243 1600 1856 2084 2359 2598 2816 3043 6031 6530 6966 7364 55 311 729 1003 1245 1604 1857 2086 2360 2599 2817 3044 6036 6531 6968 7368 56 312 731 1004 1246 1605 1858 2089 2361 2600 2818 3045 6043 6532 6969 7369 57 313 738 1005 1247 1606 1859 2090 2362 2601 2819 3046 6045 6533 6972 7370 58 315 739 1006 1248 1607 1860 2091 2363 2603 2820 3047 6048 6535 6978 7371 59 316 745 1007 1250 1608 1861 2092 2364 2604 2821 3048 6051 6540 6980 7372 60 317 765 1008 1251 1610 1862 2093 2365 2605 2822 3049 6054 6542 6982 7374 61 318 766 1009 1252 1611 1863 2094 2366 2606 2823 3050 6056 6549 6984 7377 62 319 767 1010 1253 1612 1864 2095 2367 2608 2824 3051 6057 6551 6990 7378 63 320 768 1011 1254 1616 1865 2096 2368 2610 2825 3052 6058 6552 6993 7381 64 321 769 1012 1255 1617 1866 2103 2369 2611 2826 3053 6059 6555 6998 7383 65 322 770 1013 1256 1618 1867 2104 2370 2612 2827 3054 6061 6558 6999 7384 66 323 771 1014 1257 1619 1868 2105 2371 2613 2828 3055 6063 6559 7001 7387 67 324 772 1015 1258 1620 1869 2108 2372 2614 2829 3056 6067 6561 7006 7388 68 325 773 1016 1259 1621 1870 2111 2373 2615 2830 3057 6068 6563 7009 7389 69 327 774 1017 1261 1622 1871 2112 2374 2616 2831 3058 6071 6565 7013 7393 70 328 775 1018 1262 1623 1872 2113 2375 2617 2832 3059 6072 6567 7015 7394 72 329 776 1019 1263 1625 1873 2114 2376 2618 2833 3060 6073 6568 7023 7396 73 330 780 1020 1264 1626 1874 2115 2377 2619 2834 3061 6074 6572 7024 7397 74 331 782 1021 1265 1627 1875 2117 2378 2620 2835 3062 6079 6575 7025 7402 75 332 783 1022 1266 1628 1876 2121 2379 2621 2836 3063 6080 6577 7026 7403 76 333 784 1023 1267 1629 1877 2122 2380 2622 2837 3064 6084 6578 7027 7404 77 334 789 1024 1269 1630 1878 2123 2381 2623 2838 3065 6089 6579 7030 7412 78 335 797 1025 1270 1631 1879 2125 2382 2624 2839 3066 6091 6580 7031 7415 79 336 798 1026 1272 1632 1880 2126 2383 2625 2840 3067 6093 6581 7033 7416 80 337 799 1027 1274 1633 1881 2128 2384 2626 2841 3070 6094 6582 7034 7417 81 338 800 1028 1275 1634 1882 2130 2385 2627 2842 3071 6096 6583 7035 7418 83 339 801 1029 1278 1635 1883 2132 2386 2628 2843 3072 6099 6584 7036 7419 86 340 802 1030 1279 1636 1884 2136 2387 2629 2844 3073 6103 6585 7037 7430 87 341 803 1031 1280 1638 1885 2137 2388 2630 2845 3074 6106 6587 7038 7431 88 342 804 1032 1282 1639 1886 2138 2389 2631 2846 3075 6107 6591 7043 7433 89 343 805 1033 1288 1641 1887 2141 2390 2632 2847 3076 6108 6594 7045 7434 90 344 806 1034 1290 1642 1888 2143 2391 2633 2848 3077 6112 6595 7046 7435 92 345 807 1035 1295 1644 1889 2144 2392 2634 2849 3078 6115 6596 7047 7436 94 346 808 1036 1298 1645 1890 2145 2393 2635 2850 3079 6117 6598 7048 7441 96 348 809 1037 1299 1646 1891 2147 2394 2636 2851 3080 6121 6600 7051 7443 97 349 810 1038 1301 1647 1892 2148 2395 2637 2852 3081 6123 6601 7055 7444 98 350 811 1039 1302 1648 1893 2149 2396 2638 2853 3082 6130 6602 7056 7445 99 351 812 1040 1305 1649 1894 2150 2397 2639 2854 3083 6133 6603 7058 7448 100 352 813 1041 1308 1651 1895 2152 2398 2640 2855 3084 6136 6606 7060 7449 101 353 814 1042 1311 1653 1896 2153 2399 2641 2856 3085 6139 6607 7064 7450 102 354 815 1043 1312 1656 1897 2154 2400 2642 2857 3086 6142 6608 7065 7453 103 355 816 1044 1314 1657 1898 2155 2401 2643 2858 3087 6144 6610 7067 7455 104 356 817 1045 1315 1658 1899 2156 2402 2644 2859 3088 6147 6611 7068 7458 105 357 818 1046 1320 1659 1900 2158 2403 2645 2860 3089 6148 6612 7070 7461 106 359 819 1047 1322 1661 1901 2159 2404 2646 2861 3090 6150 6615 7071 7466 107 360 820 1048 1324 1662 1902 2161 2405 2647 2862 3091 6151 6616 7072 7469 108 361 821 1049 1326 1663 1903 2162 2406 2648 2865 3092 6152 6617 7074 7471 110 362 822 1050 1327 1664 1905 2163 2407 2649 2866 3093 6155 6621 7075 7472 112 363 824 1051 1328 1665 1906 2164 2408 2650 2867 3094 6163 6622 7077 7473 113 364 825 1052 1338 1666 1907 2165 2409 2651 2868 3096 6165 6624 7078 7474 114 365 826 1053 1340 1667 1908 2166 2410 2652 2869 3097 6168 6627 7079 7476 115 367 827 1054 1342 1668 1909 2167 2411 2653 2870 3098 6171 6630 7080 7488 116 368 828 1055 1347 1669 1910 2170 2413 2654 2871 3099 6172 6635 7081 7489 117 369 829 1056 1348 1670 1911 2172 2414 2656 2872 3101 6176 6639 7082 7496 118 370 830 1057 1349 1671 1912 2173 2417 2657 2873 3102 6180 6642 7085 7497 119 371 831 1058 1350 1672 1913 2174 2418 2658 2874 3103 6185 6644 7087 7499 120 372 832 1059 1354 1673 1914 2175 2422 2659 2875 3104 6188 6645 7088 7500 121 373 833 1060 1359 1674 1915 2176 2423 2660 2877 3107 6190 6646 7089 7501 122 374 834 1061 1366 1675 1916 2177 2425 2661 2878 3108 6191 6648 7091 7508 123 376 835 1062 1369 1676 1917 2178 2426 2662 2879 3109 6193 6650 7096 7509 124 377 836 1063 1370 1677 1918 2179 2431 2663 2881 3110 6196 6651 7098 7511 125 378 837 1065 1371 1678 1920 2182 2436 2664 2882 3111 6197 6652 7100 7515 126 380 839 1066 1372 1679 1921 2184 2438 2665 2884 3112 6201 6654 7103 7519 127 382 840 1067 1373 1680 1922 2185 2440 2666 2885 3113 6204 6655 7105 7520 128 384 841 1068 1374 1681 1923 2186 2441 2667 2886 3114 6205 6656 7110 7523 129 385 842 1069 1375 1682 1924 2191 2442 2668 2887 3115 6207 6659 7115 7525 130 386 843 1070 1376 1683 1925 2192 2443 2669 2888 3116 6208 6665 7116 7526 131 388 844 1071 1377 1684 1926 2193 2444 2670 2889 3117 6211 6666 7120 7527 132 389 845 1072 1378 1685 1927 2195 2445 2671 2890 3118 6216 6668 7121 7530 133 391 846 1073 1379 1686 1929 2196 2446 2672 2891 3119 6218 6671 7122 7531 134 392 847 1074 1380 1687 1931 2197 2447 2673 2892 3120 6219 6672 7123 7536 135 394 849 1075 1381 1688 1932 2198 2448 2674 2893 3121 6223 6674 7125 7537 136 395 852 1076 1382 1689 1934 2201 2449 2675 2894 3122 6227 6675 7127 7538 137 396 853 1077 1383 1690 1935 2202 2450 2676 2895 3123 6234 6676 7128 7539 138 397 854 1078 1384 1691 1936 2205 2451 2677 2896 3124 6236 6680 7129 7540 139 398 856 1079 1385 1693 1937 2206 2452 2679 2897 3125 6240 6681 7131 7541 140 399 860 1080 1386 1694 1938 2207 2453 2680 2898 3126 6243 6683 7135 7543 141 400 861 1081 1387 1695 1939 2213 2454 2681 2900 3127 6244 6684 7136 7545 142 402 862 1082 1388 1696 1940 2214 2455 2682 2901 3128 6247 6685 7138 7547 143 403 863 1083 1389 1697 1941 2219 2456 2683 2902 3129 6248 6686 7140 7549 144 404 866 1084 1390 1698 1942 2224 2457 2684 2903 3130 6250 6688 7141 7550 145 407 867 1085 1391 1699 1943 2225 2458 2685 2904 3131 6253 6690 7142 7555 146 408 868 1086 1392 1700 1944 2226 2459 2687 2905 3133 6254 6692 7143 7556 147 409 871 1087 1393 1701 1945 2227 2460 2688 2906 3134 6257 6693 7144 7558 148 413 872 1088 1394 1702 1946 2228 2461 2689 2907 3135 6258 6695 7147 7565 149 415 873 1089 1395 1703 1947 2229 2462 2690 2908 3136 6263 6698 7148 7566 150 416 874 1090 1396 1704 1948 2230 2463 2692 2909 3138 6264 6705 7150 7567 151 423 875 1091 1397 1705 1949 2231 2464 2693 2910 3139 6265 6706 7151 7568 153 426 876 1092 1398 1706 1950 2232 2465 2695 2911 3144 6266 6708 7153 7569 154 428 877 1093 1399 1707 1951 2233 2468 2696 2912 3146 6267 6709 7154 7570 156 438 878 1094 1400 1708 1952 2234 2469 2697 2913 3149 6268 6710 7157 7574 157 449 879 1095 1401 1709 1953 2235 2470 2700 2914 3152 6269 6713 7158 7576 158 450 880 1097 1402 1710 1954 2236 2471 2701 2915 3154 6271 6715 7160 7578 159 452 881 1103 1403 1711 1955 2238 2472 2702 2916 3155 6272 6716 7163 7580 160 460 882 1115 1404 1712 1956 2239 2474 2703 2917 3157 6273 6717 7164 7582 161 461 883 1116 1405 1713 1957 2240 2477 2706 2918 3167 6275 6718 7167 7585 162 462 884 1117 1406 1714 1958 2241 2478 2708 2919 3169 6278 6719 7169 7587 164 464 885 1118 1407 1715 1959 2242 2480 2709 2920 3171 6281 6724 7170 7588 165 469 886 1120 1408 1716 1960 2244 2488 2710 2921 3172 6284 6726 7171 7589 166 470 887 1121 1409 1717 1961 2245 2489 2711 2922 3173 6285 6728 7172 7590 167 472 888 1123 1410 1718 1962 2246 2490 2712 2923 3176 6286 6730 7174 7591 168 480 889 1126 1411 1719 1963 2247 2497 2713 2925 3177 6287 6731 7175 7593 169 481 890 1131 1412 1720 1964 2248 2498 2714 2926 3180 6289 6732 7176 7594 170 483 891 1136 1413 1721 1965 2249 2503 2715 2927 3181 6290 6733 7180 7597 171 484 892 1137 1414 1722 1966 2250 2504 2716 2928 3184 6292 6736 7181 7599 172 502 893 1138 1415 1723 1967 2251 2505 2717 2929 3190 6293 6738 7184 7600 173 503 894 1139 1416 1725 1968 2252 2506 2718 2930 3196 6294 6744 7186 7606 175 504 895 1140 1417 1726 1969 2253 2507 2719 2931 3198 6300 6746 7187 7607 176 523 896 1141 1418 1729 1970 2254 2508 2720 2932 3199 6304 6751 7188 7610 180 524 897 1142 1419 1735 1971 2255 2509 2721 2933 3208 6305 6754 7189 7612 181 527 898 1143 1420 1736 1972 2256 2510 2722 2934 3214 6307 6756 7191 7613 183 534 899 1144 1421 1738 1973 2257 2511 2723 2935 3233 6309 6757 7192 7615 184 535 900 1145 1422 1739 1974 2259 2512 2724 2936 3247 6310 6758 7193 7617 185 537 901 1146 1423 1741 1975 2260 2513 2725 2937 3248 6311 6760 7194 7621 190 538 902 1147 1424 1742 1976 2261 2514 2726 2938 3251 6312 6761 7197 7625 191 539 903 1148 1425 1743 1977 2262 2515 2727 2939 3252 6313 6762 7198 7629 192 540 904 1149 1426 1747 1978 2263 2516 2728 2940 3253 6317 6765 7203 7632 194 541 905 1150 1427 1751 1979 2264 2517 2729 2941 3254 6318 6770 7204 7633 195 543 906 1151 1429 1752 1980 2265 2518 2730 2942 3256 6322 6772 7205 7634 196 544 907 1152 1430 1753 1981 2266 2519 2731 2943 3259 6323 6773 7206 7635 198 545 908 1153 1431 1754 1982 2268 2520 2732 2945 3260 6324 6776 7207 7636 199 547 909 1154 1432 1755 1983 2270 2521 2733 2947 3261 6325 6777 7209 7638 200 550 910 1155 1433 1756 1984 2271 2522 2734 2948 3262 6327 6778 7214 7644 201 553 911 1156 1434 1757 1985 2273 2523 2735 2950 3263 6328 6783 7215 7646 203 554 912 1157 1435 1758 1986 2275 2524 2736 2951 3264 6329 6784 7216 7649 205 555 913 1158 1436 1759 1987 2276 2525 2737 2953 3266 6339 6785 7217 7650 206 557 914 1159 1439 1760 1988 2277 2526 2738 2954 3268 6340 6786 7218 7651 207 559 915 1160 1440 1761 1989 2278 2527 2739 2955 3269 6343 6788 7222 7652 208 561 916 1161 1441 1762 1990 2279 2528 2740 2957 3270 6344 6793 7226 7653 209 563 917 1163 1442 1764 1991 2280 2529 2741 2959 3272 6346 6794 7227 7654 210 565 918 1164 1444 1765 1992 2282 2530 2742 2960 3277 6349 6795 7228 7656 211 567 919 1165 1446 1766 1993 2286 2531 2743 2962 3286 6351 6796 7240 7657 212 568 920 1166 1447 1767 1994 2287 2532 2744 2965 3302 6356 6797 7242 7658 213 570 921 1167 1449 1768 1995 2288 2533 2745 2966 3303 6363 6798 7243 7659 215 571 922 1168 1452 1769 1996 2291 2534 2746 2967 3305 6364 6801 7244 7660 216 572 923 1169 1455 1770 1997 2292 2535 2747 2970 3310 6367 6802 7246 7662 217 575 924 1170 1456 1771 1998 2294 2536 2748 2971 3313 6370 6808 7247 7663 218 583 925 1171 1460 1772 1999 2295 2537 2749 2972 3315 6377 6809 7250 7665 219 584 926 1172 1471 1773 2000 2299 2538 2750 2973 3316 6378 6811 7251 7667 223 585 927 1173 1497 1774 2001 2300 2539 2751 2974 3326 6381 6815 7252 7668 225 589 928 1174 1499 1775 2002 2301 2540 2752 2975 3329 6384 6816 7253 7670 227 590 929 1176 1504 1776 2003 2302 2541 2755 2976 4501 6387 6823 7255 7674 228 591 931 1177 1505 1777 2004 2303 2542 2756 2977 4502 6389 6826 7258 7675 229 592 933 1178 1506 1778 2005 2304 2543 2757 2979 4503 6394 6827 7261 7676 230 594 934 1179 1507 1779 2006 2305 2544 2758 2980 4505 6395 6832 7262 7677 232 595 936 1181 1508 1780 2007 2306 2545 2760 2981 4506 6402 6834 7263 7679 234 596 937 1184 1519 1781 2008 2307 2546 2761 2982 4507 6403 6841 7264 7681 235 597 938 1185 1521 1783 2009 2308 2547 2762 2983 4508 6407 6842 7267 7682 236 598 939 1186 1523 1784 2011 2309 2548 2764 2984 4509 6409 6845 7273 7685 237 599 944 1187 1527 1785 2012 2310 2549 2765 2985 4510 6410 6850 7274 7694 238 600 945 1190 1529 1786 2013 2311 2550 2766 2986 4511 6412 6852 7275 7695 239 602 946 1193 1539 1787 2014 2312 2551 2767 2987 4512 6415 6855 7276 7698 240 604 948 1197 1540 1788 2015 2313 2552 2768 2988 4513 6417 6859 7280 7702 241 605 950 1198 1541 1789 2017 2314 2553 2769 2989 4514 6418 6861 7281 7706 242 606 951 1199 1542 1790 2018 2315 2554 2772 2990 4515 6419 6864 7282 7707 243 607 952 1200 1543 1792 2019 2316 2555 2773 2991 4516 6421 6866 7284 7714 244 610 957 1201 1544 1793 2020 2317 2556 2774 2992 4517 6423 6870 7286 7717 245 613 958 1202 1545 1794 2021 2318 2557 2775 2993 4518 6424 6872 7288 7719 248 614 959 1203 1546 1795 2022 2319 2558 2776 2994 4519 6425 6873 7290 7723 249 616 960 1204 1547 1796 2023 2320 2559 2777 2995 4520 6426 6874 7291 7724 252 617 961 1205 1548 1799 2024 2321 2560 2778 2997 4521 6427 6876 7292 7728 253 618 962 1206 1549 1801 2025 2322 2561 2779 2998 4522 6429 6877 7293 254 624 963 1207 1550 1802 2027 2323 2562 2780 2999 4523 6432 6878 7294

A further analysis identified a subset of approximately 320 gene modifying polypeptide candidates having a Z-score of at least 1 or greater across all of conditions 1, 2, and 3. These results show that this subset of gene modifying polypeptides had editing activity in all analyzed conditions of the screening assay (FIG. 14 , magenta colored dots). These include gene modifying polypeptides having amino acid sequences according to any one of the SEQ ID NOs listed in Table D2 below.

TABLE D2 Gene modifying polypeptide candidates having a Z-score of at least 1 or greater across all of conditions 1, 2, and 3. SEQ ID NOs 34 874 1377 1945 2370 2711 3014 35 878 1380 1953 2371 2712 3015 36 882 1381 1961 2449 2713 3018 37 883 1382 1970 2503 2714 3026 38 884 1383 1976 2504 2715 3035 39 890 1384 1992 2505 2718 3039 40 900 1385 2048 2506 2721 3042 41 901 1389 2086 2507 2726 3053 49 912 1390 2091 2508 2734 3059 62 958 1394 2093 2510 2780 3067 97 960 1397 2115 2511 2781 3076 113 963 1400 2144 2512 2782 3079 117 964 1401 2158 2513 2783 3084 121 966 1404 2192 2514 2784 3091 139 987 1405 2225 2515 2787 3093 140 1006 1406 2227 2518 2788 3094 141 1007 1410 2231 2519 2789 3096 142 1008 1540 2299 2521 2790 3108 190 1012 1543 2300 2525 2792 3111 191 1015 1550 2301 2526 2794 3112 192 1016 1616 2302 2527 2795 3116 195 1017 1618 2303 2528 2797 3120 199 1018 1619 2304 2530 2798 3125 212 1019 1666 2305 2534 2800 3126 213 1020 1668 2308 2536 2801 3130 228 1022 1672 2309 2542 2802 232 1023 1677 2311 2544 2804 239 1025 1679 2312 2548 2813 268 1038 1682 2314 2559 2817 303 1049 1686 2315 2568 2818 313 1059 1754 2316 2610 2826 316 1137 1759 2317 2611 2835 318 1168 1770 2319 2612 2865 332 1171 1856 2322 2614 2874 341 1197 1857 2323 2615 2877 363 1198 1861 2325 2618 2886 396 1202 1863 2326 2619 2888 480 1203 1864 2327 2622 2890 550 1216 1865 2328 2623 2895 590 1219 1868 2329 2624 2901 647 1225 1870 2331 2627 2904 715 1235 1877 2335 2629 2920 800 1242 1883 2338 2632 2932 801 1371 1889 2342 2633 2937 804 1372 1937 2346 2636 2943 806 1373 1938 2353 2638 2950 871 1374 1940 2363 2644 2966 872 1375 1942 2364 2648 2972 873 1376 1943 2365 2653 2982

Additional sequencing data were generated for same DNA libraries for the test template g10 condition in HEK293T cells (condition 3) to improve detection sensitivity and confidence in evidence of genome editing activity. This further analysis including the revised dataset for condition 3 identified a subset of approximately 420 gene modifying polypeptide candidates having a Z score of at least 1 or greater across all of conditions 1, 2, and 3. These results show that this subset of gene modifying polypeptides had editing activity in all conditions of the screening assay under this revised analysis. These include gene modifying polypeptides having amino acid sequences according to any one of the SEQ ID NOs listed in Table D3 below.

TABLE D3 Gene modifying polypeptide candidates having a Z-score of at least 1 or greater across all of conditions 1, 2, or 3. SEQ ID NOs: 34 961 1616 2301 2568 2822 4522 35 963 1618 2302 2578 2826 4532 36 964 1619 2303 2585 2833 6312 37 966 1666 2304 2592 2835 6505 38 967 1672 2305 2610 2838 6761 39 978 1679 2308 2611 2840 6925 48 1006 1682 2309 2612 2865 7036 49 1007 1686 2311 2614 2871 7067 62 1008 1690 2312 2615 2874 7397 97 1012 1691 2314 2618 2877 113 1015 1695 2315 2619 2878 121 1016 1698 2316 2622 2886 123 1017 1721 2317 2623 2887 139 1018 1754 2319 2624 2888 140 1019 1759 2322 2627 2890 142 1020 1769 2323 2629 2895 144 1022 1770 2325 2632 2901 147 1023 1772 2326 2633 2904 190 1025 1773 2327 2636 2905 191 1029 1856 2328 2638 2909 192 1038 1857 2329 2639 2920 195 1043 1861 2331 2644 2922 213 1049 1863 2335 2647 2928 219 1052 1864 2338 2648 2932 232 1059 1865 2342 2649 2937 239 1061 1868 2347 2653 2943 252 1115 1870 2353 2654 2948 258 1137 1874 2363 2666 2950 268 1168 1877 2364 2667 2966 303 1171 1881 2365 2675 2967 316 1197 1883 2370 2676 2972 318 1198 1889 2371 2681 2976 320 1202 1899 2382 2711 2982 332 1203 1937 2395 2712 2991 363 1210 1938 2403 2713 3014 384 1216 1939 2449 2714 3015 386 1219 1940 2503 2715 3018 392 1225 1942 2504 2716 3026 396 1235 1943 2505 2718 3035 480 1242 1945 2506 2721 3039 550 1371 1953 2507 2723 3042 590 1373 1961 2508 2726 3052 647 1374 1968 2510 2731 3053 715 1375 1970 2511 2734 3059 800 1376 1976 2512 2744 3067 801 1377 1978 2513 2745 3076 804 1380 1991 2514 2780 3079 805 1381 1992 2515 2781 3084 806 1382 2048 2518 2782 3087 818 1383 2086 2519 2783 3091 819 1384 2091 2521 2784 3093 871 1385 2092 2525 2787 3094 872 1389 2093 2526 2788 3096 873 1390 2115 2527 2789 3108 874 1394 2137 2528 2790 3111 876 1397 2144 2530 2791 3112 878 1399 2148 2531 2792 3116 880 1400 2158 2534 2794 3120 883 1401 2172 2536 2795 3121 884 1402 2174 2542 2797 3124 890 1405 2192 2544 2798 3125 898 1406 2225 2547 2800 3126 900 1410 2226 2548 2801 3130 901 1415 2227 2551 2802 3136 912 1419 2231 2556 2804 4505 915 1422 2235 2559 2808 4508 929 1424 2236 2561 2813 4514 958 1543 2299 2562 2817 4519 960 1550 2300 2566 2818 4521

Approximately 3680 gene modifying polypeptide candidates within the library had a Z-score of at least 1 or greater in any one of conditions 1, 2, or 3 using this further analysis. These results show that this subset of gene modifying polypeptides had editing activity in at least one analyzed condition of the screening assay under this revised analysis. The subset of these gene modifying polypeptides are encoded by amino acid sequences of any one of the SEQ ID NOs listed in Table D4 below.

TABLE D4 Gene modifying polypeptide candidates having a Z-score of at least 1 or greater in any one of conditions 1, 2, or 3 according to the above further analysis. SEQ ID NOs: 1 343 846 1197 1624 1955 2294 2616 2929 4523 6495 7046 7570 2 344 847 1198 1625 1956 2295 2617 2930 4524 6497 7047 7574 3 345 848 1199 1626 1957 2299 2618 2931 4525 6499 7049 7575 4 346 849 1200 1627 1958 2300 2619 2932 4526 6501 7050 7576 5 348 850 1201 1628 1959 2301 2620 2933 4527 6502 7051 7580 6 349 852 1202 1629 1960 2302 2621 2934 4528 6503 7052 7582 7 350 853 1203 1630 1961 2303 2622 2935 4529 6505 7053 7585 9 351 854 1204 1631 1962 2304 2623 2936 4530 6506 7055 7587 10 352 855 1205 1632 1963 2305 2624 2937 4531 6511 7056 7588 12 353 856 1206 1633 1964 2306 2625 2938 4532 6512 7058 7590 13 354 857 1207 1634 1965 2307 2626 2939 4533 6515 7059 7591 14 355 860 1208 1635 1966 2308 2627 2940 4534 6524 7060 7592 17 356 861 1209 1636 1967 2309 2628 2941 4535 6525 7062 7595 18 357 862 1210 1637 1968 2310 2629 2942 4536 6526 7063 7596 19 358 863 1211 1638 1969 2311 2630 2943 4537 6527 7064 7597 22 359 866 1212 1639 1970 2312 2631 2944 4538 6529 7065 7599 24 360 867 1213 1640 1971 2313 2632 2945 4539 6530 7067 7600 28 361 868 1214 1641 1972 2314 2633 2946 4540 6531 7068 7603 33 362 869 1215 1642 1973 2315 2634 2947 4541 6532 7070 7606 34 363 870 1216 1644 1974 2316 2635 2948 6001 6533 7072 7607 35 364 871 1217 1645 1975 2317 2636 2950 6004 6535 7073 7610 36 365 872 1218 1646 1976 2318 2637 2951 6007 6538 7074 7612 37 366 873 1219 1648 1977 2319 2638 2952 6008 6540 7075 7613 38 367 874 1220 1649 1978 2320 2639 2953 6010 6542 7078 7615 39 368 875 1221 1651 1979 2321 2640 2954 6012 6543 7079 7620 40 369 876 1222 1652 1980 2322 2641 2955 6013 6544 7080 7621 41 370 877 1223 1653 1981 2323 2642 2957 6014 6545 7081 7624 42 371 878 1224 1654 1982 2324 2643 2958 6015 6549 7082 7625 43 372 879 1225 1655 1983 2325 2644 2959 6021 6551 7084 7626 44 373 880 1226 1656 1984 2326 2645 2960 6022 6552 7085 7629 45 374 881 1227 1657 1985 2327 2646 2962 6023 6555 7087 7631 46 375 882 1228 1658 1986 2328 2647 2965 6025 6557 7088 7632 47 376 883 1229 1659 1987 2329 2648 2966 6026 6559 7089 7633 48 377 884 1230 1660 1988 2330 2649 2967 6028 6561 7091 7634 49 380 885 1231 1661 1989 2331 2650 2968 6029 6563 7092 7635 50 382 886 1232 1662 1990 2332 2651 2969 6030 6564 7095 7636 51 383 887 1233 1663 1991 2333 2652 2971 6031 6565 7096 7638 52 384 888 1234 1664 1992 2334 2653 2972 6036 6566 7098 7643 53 385 889 1235 1665 1993 2335 2654 2973 6038 6567 7100 7644 54 386 890 1236 1666 1994 2336 2655 2974 6040 6568 7103 7646 55 387 891 1237 1667 1995 2337 2656 2975 6041 6572 7104 7649 56 388 892 1238 1668 1996 2338 2657 2976 6043 6575 7105 7650 57 389 893 1239 1669 1997 2339 2658 2979 6045 6577 7109 7651 58 391 894 1240 1670 1998 2340 2659 2981 6048 6579 7110 7652 59 392 895 1241 1671 1999 2341 2660 2982 6049 6580 7111 7653 60 393 896 1242 1672 2000 2342 2661 2983 6051 6581 7114 7654 61 394 897 1243 1673 2001 2343 2662 2984 6054 6582 7115 7656 62 395 898 1244 1674 2002 2344 2663 2985 6055 6583 7116 7657 63 396 899 1245 1675 2003 2345 2664 2986 6056 6584 7120 7658 64 397 900 1246 1676 2004 2346 2665 2987 6057 6585 7121 7659 65 398 901 1247 1677 2005 2347 2666 2988 6058 6587 7123 7660 66 399 902 1248 1678 2006 2348 2667 2989 6059 6589 7125 7662 67 400 903 1249 1679 2007 2349 2668 2990 6060 6590 7127 7663 68 401 904 1250 1680 2008 2350 2669 2991 6061 6591 7128 7665 69 402 905 1251 1681 2009 2351 2670 2992 6063 6594 7129 7667 70 403 906 1252 1682 2010 2352 2671 2993 6064 6595 7131 7668 71 404 907 1253 1683 2011 2353 2672 2994 6067 6596 7133 7669 72 406 908 1254 1684 2012 2354 2673 2995 6068 6598 7134 7670 73 407 909 1255 1685 2013 2355 2674 2997 6069 6600 7135 7674 74 408 910 1256 1686 2014 2356 2675 2998 6071 6601 7136 7675 75 409 911 1257 1687 2015 2357 2676 2999 6072 6602 7140 7676 76 410 912 1258 1688 2017 2358 2677 3001 6073 6603 7141 7677 77 413 913 1259 1689 2018 2359 2678 3002 6074 6606 7142 7679 78 415 914 1261 1690 2019 2360 2679 3003 6076 6607 7143 7681 79 416 915 1262 1691 2020 2361 2680 3004 6079 6608 7144 7682 80 419 916 1263 1692 2021 2362 2681 3005 6080 6609 7147 7685 81 420 917 1264 1693 2022 2363 2682 3006 6081 6610 7148 7686 82 421 918 1265 1694 2023 2364 2683 3007 6083 6611 7149 7689 83 424 919 1266 1695 2024 2365 2684 3008 6084 6612 7150 7693 85 426 920 1267 1696 2025 2366 2685 3009 6089 6613 7151 7694 86 427 921 1269 1697 2026 2367 2687 3010 6090 6614 7153 7695 87 428 922 1270 1698 2027 2368 2688 3011 6091 6615 7154 7698 88 429 923 1271 1699 2028 2369 2689 3012 6092 6617 7155 7700 89 432 924 1272 1700 2029 2370 2690 3014 6093 6618 7156 7701 90 433 925 1273 1701 2030 2371 2691 3015 6094 6619 7158 7702 91 438 926 1274 1702 2031 2372 2692 3016 6096 6621 7159 7706 92 441 927 1275 1703 2033 2373 2693 3018 6097 6622 7160 7707 94 446 928 1277 1704 2034 2374 2694 3019 6099 6623 7163 7708 95 449 929 1278 1705 2035 2375 2695 3020 6103 6624 7164 7713 96 450 930 1279 1706 2036 2376 2697 3021 6105 6625 7167 7715 97 452 931 1280 1707 2037 2377 2698 3022 6106 6627 7169 7717 98 460 932 1282 1708 2038 2378 2699 3023 6107 6629 7170 7719 99 461 933 1288 1709 2039 2379 2700 3025 6108 6630 7171 7721 100 462 934 1290 1710 2040 2380 2701 3026 6112 6632 7172 7722 101 464 936 1295 1711 2041 2381 2702 3027 6115 6635 7174 7723 102 465 937 1296 1712 2042 2382 2703 3028 6117 6639 7175 7724 103 469 938 1298 1713 2043 2383 2704 3029 6121 6642 7176 7726 104 470 939 1299 1714 2044 2384 2708 3030 6122 6644 7180 7727 105 472 940 1301 1715 2045 2385 2709 3031 6123 6645 7181 7729 106 475 942 1302 1716 2046 2386 2710 3033 6129 6646 7184 7730 107 476 943 1304 1717 2047 2387 2711 3034 6130 6648 7186 7731 108 480 944 1305 1718 2048 2388 2712 3035 6133 6650 7187 7732 110 481 945 1308 1719 2049 2389 2713 3036 6136 6651 7188 7737 112 483 946 1311 1720 2050 2390 2714 3037 6138 6652 7191 7740 113 484 948 1312 1721 2051 2391 2715 3038 6139 6654 7192 7741 114 486 950 1314 1722 2052 2392 2716 3039 6142 6655 7194 115 488 951 1315 1723 2053 2393 2717 3040 6143 6656 7196 116 489 952 1320 1725 2054 2394 2718 3041 6144 6659 7197 117 495 957 1322 1726 2055 2395 2719 3042 6147 6664 7198 118 502 958 1324 1728 2056 2396 2720 3043 6148 6665 7201 119 503 959 1326 1729 2057 2397 2721 3044 6150 6666 7203 120 50 960 1327 1730 2058 2398 2722 3045 6151 6671 7204 121 510 961 1328 1731 2059 2399 2723 3046 6152 6674 7206 122 517 962 1329 1733 2060 2400 2724 3047 6153 6675 7209 123 522 963 1338 1734 2061 2401 2725 3048 6155 6676 7212 124 523 964 1340 1735 2062 2402 2726 3049 6158 6679 7214 125 524 965 1342 1736 2063 2403 2727 3050 6160 6680 7215 126 527 966 1346 1737 2064 2404 2728 3051 6164 6681 7216 127 534 967 1347 1738 2066 2405 2729 3052 6165 6683 7217 128 535 968 1348 1739 2069 2406 2730 3053 6168 6684 7218 129 536 969 1349 1741 2070 2407 2731 3054 6169 6685 7220 130 537 970 1350 1742 2071 2408 2732 3055 6171 6686 7221 131 538 971 1351 1743 2072 2409 2733 3056 6172 6687 7222 132 539 972 1354 1744 2074 2410 2734 3057 6173 6688 7226 133 540 973 1359 1745 2075 2411 2735 3058 6174 6690 7227 134 541 974 1362 1747 2076 2412 2736 3059 6175 6691 7228 135 542 975 1365 1748 2079 2413 2737 3060 6176 6692 7230 136 543 976 1366 1750 2080 2414 2738 3061 6177 6693 7232 137 544 977 1369 1751 2081 2415 2739 3062 6178 6695 7236 138 545 978 1370 1752 2082 2416 2740 3063 6179 6698 7240 139 546 979 1371 1753 2084 2417 2741 3064 6180 6705 7242 140 547 980 1372 1754 2086 2418 2742 3065 6181 6706 7243 141 548 981 1373 1755 2089 2419 2743 3066 6182 6708 7244 142 549 982 1374 1756 2090 2420 2744 3067 6184 6709 7246 143 550 983 1375 1757 2091 2422 2745 3070 6185 6713 7247 144 553 984 1376 1758 2092 2423 2746 3071 6188 6715 7250 145 554 985 1377 1759 2093 2424 2747 3072 6189 6716 7251 146 555 986 1378 1760 2094 2425 2748 3073 6190 6717 7252 147 556 987 1379 1761 2095 2426 2750 3074 6191 6718 7253 148 557 988 1380 1762 2096 2427 2751 3075 6193 6719 7255 149 558 989 1381 1764 2097 2431 2752 3076 6196 6720 7258 150 559 990 1382 1765 2098 2436 2753 3077 6197 6722 7260 151 560 991 1383 1766 2099 2438 2754 3078 6200 6724 7261 153 561 992 1384 1767 2100 2440 2755 3079 6201 6726 7262 154 562 993 1385 1769 2101 2441 2756 3080 6203 6728 7263 155 563 994 1386 1770 2102 2442 2757 3081 6204 6730 7264 156 565 996 1387 1771 2103 2443 2758 3082 6205 6731 7266 157 566 997 1388 1772 2104 2444 2759 3083 6207 6732 7267 158 567 999 1389 1773 2105 2445 2760 3084 6208 6733 7273 159 568 1000 1390 1774 2106 2446 2761 3085 6215 6736 7274 160 570 1001 1391 1775 2107 2447 2762 3086 6216 6738 7275 161 571 1003 1392 1776 2108 2448 2763 3087 6218 6744 7276 162 572 1004 1393 1777 2109 2449 2764 3088 6219 6746 7281 163 575 1006 1394 1778 2111 2450 2765 3089 6223 6750 7282 164 581 1007 1395 1779 2112 2451 2766 3090 6227 6751 7284 165 583 1008 1396 1780 2113 2452 2767 3091 6234 6754 7286 166 584 1009 1397 1781 2114 2453 2768 3092 6235 6756 7288 167 585 1010 1398 1782 2115 2454 2769 3093 6236 6757 7291 168 587 1011 1399 1783 2116 2455 2771 3094 6237 6758 7292 169 589 1012 1400 1784 2117 2456 2772 3096 6240 6760 7293 170 590 1013 1401 1785 2118 2457 2773 3097 6244 6761 7294 171 591 1014 1402 1786 2119 2458 2774 3098 6247 6762 7297 172 592 1015 1403 1787 2120 2459 2775 3099 6248 6765 7298 173 593 1016 1404 1788 2121 2460 2776 3100 6250 6772 7299 174 594 1017 1405 1789 2122 2461 2778 3101 6253 6773 7301 175 595 1018 1406 1790 2123 2462 2779 3102 6254 6774 7302 176 596 1019 1407 1792 2125 2463 2780 3103 6255 6776 7303 178 597 1020 1408 1793 2126 2464 2781 3104 6257 6777 7305 179 598 1021 1409 1794 2128 2465 2782 3107 6258 6778 7306 180 599 1022 1410 1795 2129 2466 2783 3108 6263 6782 7307 181 600 1023 1411 1796 2130 2467 2784 3109 6264 6783 7311 182 601 1024 1412 1797 2132 2468 2785 3110 6265 6784 7312 183 602 1025 1413 1799 2133 2469 2786 3111 6266 6785 7313 184 604 1026 1414 1800 2135 2470 2787 3112 6267 6786 7317 185 605 1027 1415 1801 2136 2471 2788 3113 6268 6788 7320 186 606 1028 1416 1802 2137 2472 2789 3114 6269 6792 7322 187 607 1029 1417 1803 2138 2473 2790 3115 6271 6793 7323 188 610 1030 1418 1804 2140 2474 2791 3116 6272 6794 7326 190 611 1031 1419 1805 2141 2476 2792 3117 6273 6795 7327 191 614 1032 1420 1806 2142 2477 2793 3118 6275 6796 7328 192 616 1033 1421 1808 2143 2478 2794 3119 6277 6797 7329 194 617 1034 1422 1809 2144 2479 2795 3120 6278 6798 7331 195 618 1035 1423 1810 2145 2480 2796 3121 6279 6800 7335 196 624 1036 1424 1811 2146 2481 2797 3122 6280 6801 7336 197 625 1037 1425 1812 2147 2482 2798 3123 6281 6802 7339 198 628 1038 1426 1813 2148 2483 2799 3124 6282 6803 7342 199 631 1039 1427 1815 2149 2484 2800 3125 6284 6808 7343 200 633 1040 1428 1816 2150 2485 2801 3126 6285 6809 7345 201 634 1041 1429 1818 2151 2488 2802 3127 6286 6811 7346 203 636 1042 1430 1819 2152 2489 2803 3128 6287 6815 7347 204 645 1043 1431 1824 2153 2490 2804 3129 6288 6822 7348 205 647 1044 1432 1825 2154 2491 2805 3130 6290 6824 7349 206 648 1045 1433 1827 2155 2492 2806 3131 6292 6826 7350 207 649 1046 1434 1828 2156 2497 2807 3133 6293 6827 7352 208 650 1047 1435 1829 2158 2498 2808 3134 6294 6829 7357 209 652 1048 1436 1831 2159 2501 2809 3135 6298 6832 7358 210 653 1049 1437 1834 2161 2502 2810 3136 6299 6833 7360 211 654 1050 1439 1835 2162 2503 2811 3138 6304 6834 7361 212 655 1051 1440 1838 2163 2504 2812 3139 6305 6835 7362 213 656 1052 1441 1840 2164 2505 2813 3141 6307 6837 7364 214 657 1053 1442 1842 2165 2506 2814 3142 6308 6841 7368 215 659 1054 1443 1843 2166 2507 2815 3144 6309 6842 7369 216 661 1055 1444 1844 2167 2508 2816 3146 6310 6845 7370 217 662 1056 1445 1845 2168 2509 2817 3152 6311 6850 7371 218 663 1057 1446 1846 2170 2510 2818 3153 6312 6852 7372 219 664 1058 1447 1847 2171 2511 2819 3154 6313 6855 7374 220 666 1059 1449 1848 2172 2512 2820 3155 6314 6857 7375 222 667 1060 1450 1849 2173 2513 2821 3157 6315 6858 7377 223 668 1061 1451 1850 2174 2514 2822 3162 6317 6859 7378 225 669 1062 1452 1851 2175 2515 2823 3166 6319 6861 7379 226 670 1063 1455 1852 2176 2516 2824 3167 6320 6863 7380 227 673 1064 1456 1853 2177 2517 2825 3169 6322 6864 7381 228 677 1065 1460 1855 2178 2518 2826 3171 6324 6865 7384 229 678 1066 1462 1856 2179 2519 2827 3172 6325 6866 7387 230 679 1067 1471 1857 2180 2520 2828 3173 6327 6867 7388 232 680 1068 1473 1858 2182 2521 2829 3175 6328 6868 7389 234 681 1069 1475 1859 2183 2522 2830 3176 6329 6869 7390 235 687 1070 1488 1860 2184 2523 2831 3177 6334 6870 7392 236 689 1071 1489 1861 2185 2524 2832 3180 6335 6872 7393 237 690 1072 1491 1862 2186 2525 2833 3181 6339 6873 7394 238 692 1073 1492 1863 2188 2526 2834 3183 6340 6874 7396 239 694 1074 1493 1864 2189 2527 2835 3184 6343 6876 7397 240 700 1075 1497 1865 2190 2528 2836 3188 6344 6877 7400 241 702 1076 1499 1866 2191 2529 2837 3190 6345 6878 7402 242 706 1077 1504 1867 2192 2530 2838 3196 6347 6879 7403 243 711 1078 1505 1868 2193 2531 2839 3198 6349 6881 7404 244 715 1079 1506 1869 2194 2532 2840 3199 6350 6882 7412 245 716 1080 1507 1870 2195 2533 2841 3201 6351 6883 7413 248 717 1081 1508 1871 2196 2534 2842 3202 6352 6885 7415 249 720 1082 1510 1872 2197 2535 2843 3203 6353 6886 7416 251 724 1083 1513 1873 2198 2536 2844 3204 6355 6890 7417 252 726 1084 1515 1874 2199 2537 2845 3205 6356 6891 7418 253 727 1085 1519 1875 2200 2538 2846 3206 6358 6892 7419 254 729 1086 1521 1876 2201 2539 2847 3207 6359 6894 7424 255 731 1087 1523 1877 2202 2540 2848 3208 6360 6896 7430 256 738 1088 1524 1878 2204 2541 2849 3209 6363 6897 7431 257 739 1089 1527 1879 2205 2542 2850 3211 6364 6898 7433 258 740 1090 1529 1880 2206 2543 2851 3213 6366 6902 7434 259 745 1091 1531 1881 2207 2544 2852 3214 6367 6906 7435 261 747 1092 1539 1882 2210 2545 2853 3219 6370 6907 7436 262 755 1093 1540 1883 2211 2546 2854 3220 6374 6908 7441 263 756 1094 1541 1884 2212 2547 2855 3223 6377 6910 7442 264 759 1095 1542 1885 2213 2548 2856 3225 6378 6911 7443 265 765 1097 1543 1886 2214 2549 2857 3228 6380 6915 7444 268 766 1103 1544 1887 2218 2550 2858 3233 6381 6917 7445 269 767 1110 1545 1888 2219 2551 2859 3235 6384 6919 7448 270 768 1115 1546 1889 2222 2552 2860 3240 6389 6920 7449 271 769 1116 1547 1890 2223 2553 2861 3247 6390 6923 7450 272 770 1117 1548 1891 2224 2554 2862 3248 6393 6925 7452 273 771 1118 1549 1892 2225 2555 2864 3251 6394 6928 7453 274 772 1119 1550 1893 2226 2556 2865 3252 6395 6930 7455 275 773 1120 1551 1894 2227 2557 2866 3253 6396 6931 7458 276 774 1121 1552 1895 2228 2558 2867 3254 6397 6932 7461 277 775 1122 1553 1896 2229 2559 2868 3256 6402 6933 7466 278 776 1124 1554 1897 2230 2560 2869 3259 6403 6934 7469 279 780 1126 1555 1898 2231 2561 2870 3260 6407 6939 7471 280 782 1131 1556 1899 2232 2562 2871 3261 6409 6942 7472 281 783 1134 1557 1900 2233 2563 2872 3262 6410 6943 7473 283 784 1136 1558 1901 2234 2564 2873 3263 6411 6944 7474 284 789 1137 1559 1902 2235 2565 2874 3264 6412 6948 7476 285 790 1138 1560 1903 2236 2566 2875 3266 6415 6950 7477 286 797 1139 1561 1904 2237 2567 2876 3268 6417 6951 7479 287 798 1140 1563 1905 2238 2568 2877 3269 6418 6952 7483 290 799 1141 1564 1906 2239 2569 2878 3270 6419 6954 7485 293 800 1142 1565 1907 2240 2570 2880 3272 6420 6961 7488 294 801 1143 1566 1908 2241 2571 2881 3276 6421 6965 7489 295 802 1144 1567 1909 2242 2572 2882 3277 6423 6966 7493 296 803 1145 1568 1910 2244 2573 2884 3279 6424 6968 7496 297 804 1146 1570 1911 2245 2574 2885 3282 6425 6969 7497 298 805 1147 1571 1912 2246 2575 2886 3283 6426 6972 7499 300 806 1148 1572 1913 2247 2576 2887 3286 6427 6974 7500 301 807 1149 1573 1914 2248 2577 2888 3294 6431 6978 7501 302 808 1150 1574 1915 2249 2578 2889 3296 6432 6979 7502 303 809 1151 1575 1916 2250 2579 2890 3298 6433 6980 7507 304 810 1152 1576 1917 2251 2580 2891 3300 6434 6982 7508 305 811 1153 1577 1918 2252 2581 2892 3302 6435 6984 7509 306 812 1154 1578 1920 2253 2582 2893 3303 6439 6985 7510 308 813 1155 1579 1921 2254 2583 2894 3305 6440 6990 7511 309 814 1156 1580 1922 2255 2584 2895 3306 6441 6993 7513 310 815 1157 1581 1923 2256 2585 2896 3310 6442 6998 7515 312 816 1158 1582 1924 2257 2586 2897 3313 6443 6999 7516 313 817 1159 1583 1925 2259 2587 2898 3315 6444 7001 7518 315 818 1160 1584 1926 2260 2588 2900 3316 6445 7003 7519 316 819 1161 1585 1927 2261 2589 2901 3318 6449 7005 7520 317 820 1162 1588 1928 2262 2590 2903 3323 6451 7006 7523 318 821 1163 1590 1929 2263 2591 2904 3326 6453 7008 7525 319 822 1164 1592 1931 2264 2592 2905 3329 6454 7009 7526 320 823 1165 1593 1932 2265 2593 2906 4501 6455 7012 7529 321 824 1166 1594 1934 2266 2594 2907 4502 6456 7013 7530 322 825 1167 1597 1935 2268 2595 2908 4503 6457 7014 7532 323 826 1168 1598 1936 2270 2596 2909 4504 6458 7015 7536 324 827 1169 1599 1937 2271 2597 2910 4505 6459 7017 7537 325 828 1170 1600 1938 2272 2598 2911 4506 6460 7021 7538 327 829 1171 1604 1939 2273 2599 2912 4507 6461 7023 7540 328 830 1172 1605 1940 2274 2600 2913 4508 6462 7024 7541 329 831 1173 1606 1941 2275 2601 2914 4509 6465 7025 7545 330 832 1174 1607 1942 2276 2602 2915 4510 6467 7026 7547 331 833 1176 1608 1943 2277 2603 2916 4511 6469 7027 7548 332 834 1177 1610 1944 2278 2604 2917 4512 6474 7030 7549 333 835 1178 1611 1945 2279 2605 2918 4513 6476 7031 7550 334 836 1181 1612 1946 2280 2606 2919 4514 6477 7033 7555 335 837 1182 1616 1947 2281 2607 2920 4515 6478 7034 7556 336 839 1184 1617 1948 2282 2608 2921 4516 6479 7035 7558 337 840 1185 1618 1949 2286 2610 2922 4517 6480 7036 7560 338 841 1186 1619 1950 2287 2611 2923 4518 6486 7037 7562 339 842 1187 1620 1951 2288 2612 2925 4519 6488 7038 7565 340 843 1188 1621 1952 2289 2613 2926 4520 6491 7040 7566 341 844 1190 1622 1953 2291 2614 2927 4521 6492 7043 7567 342 845 1193 1623 1954 2293 2615 2928 4522 6493 7045 7569

Sequencing libraries were re-generated for the original DNA extracted from the test template g10 in U2OS cells (condition 4) and yielded a new dataset amenable to integration into the analyses of genome editing activity. The expanded analysis identified a subset of approximately 200 gene modifying polypeptide candidates having a Z-score of at least 1 or greater across all of conditions 1, 2, 3, and 4. These results show that this subset of gene modifying polypeptides had editing activity in all conditions of the screening assay under this revised analysis. These include gene modifying polypeptides having amino acid sequences according to any one of the SEQ ID NOs listed in Table D5 below.

TABLE D5 Gene modifying polypeptide candidates having a Z-score of at least 1 or greater in all of conditions 1, 2, 3, and 4. SEQ ID NOs 34 1012 1415 2309 2515 2675 2928 36 1016 1419 2314 2519 2681 2932 37 1017 1422 2316 2526 2731 2937 39 1018 1666 2319 2536 2780 2943 123 1019 1686 2322 2542 2782 2948 140 1022 1690 2325 2544 2784 2950 142 1023 1691 2326 2551 2787 3053 190 1029 1863 2327 2556 2789 3059 192 1038 1870 2328 2566 2791 3067 232 1052 1937 2329 2578 2800 3076 252 1059 1939 2331 2585 2801 3093 303 1061 1940 2338 2592 2802 3108 316 1137 1942 2342 2610 2804 3111 332 1198 1953 2347 2611 2813 3116 386 1210 1961 2353 2612 2817 3120 647 1225 1968 2363 2615 2826 3121 800 1242 1970 2364 2618 2833 3124 804 1371 1976 2365 2623 2835 3126 876 1374 1978 2371 2624 2838 3130 878 1375 2048 2382 2627 2865 4514 880 1376 2086 2395 2629 2874 4519 884 1382 2093 2403 2632 2877 4522 901 1383 2137 2449 2633 2887 6761 915 1384 2172 2504 2636 2888 6925 929 1385 2174 2505 2638 2890 7067 961 1390 2300 2508 2639 2901 964 1394 2301 2510 2644 2904 967 1397 2302 2511 2647 2909 1006 1400 2303 2512 2666 2922

Approximately 4030 gene modifying polypeptide candidates within the library had a Z-score of at least 1 or greater in any one of conditions 1, 2, 3, or 4 using this further analysis. These results show that this subset of gene modifying polypeptides had editing activity in at least one analyzed condition of the screening assay under this revised analysis. The subset of these gene modifying polypeptides are encoded by amino acid sequences of any one of the SEQ ID NOs listed in Table D6 below.

TABLE D6 Gene modifying polypeptide candidates having a Z-score of at least 1 or greater in any one of conditions 1, 2, 3, or 4. SEQ ID NOs: 1 486 1065 1642 2097 2560 2994 6192 6784 7361 2 488 1066 1644 2098 2561 2995 6193 6785 7362 3 489 1067 1645 2099 2562 2997 6195 6786 7364 4 495 1068 1646 2100 2563 2998 6196 6787 7368 5 499 1069 1648 2101 2564 2999 6197 6788 7369 6 502 1070 1649 2102 2565 3001 6200 6791 7370 7 503 1071 1651 2103 2566 3002 6201 6792 7371 9 504 1072 1652 2104 2567 3003 6203 6793 7372 10 510 1073 1653 2105 2568 3004 6204 6794 7374 12 517 1074 1654 2106 2569 3005 6205 6795 7375 13 522 1075 1655 2107 2570 3006 6206 6796 7377 14 523 1076 1656 2108 2571 3007 6207 6797 7378 17 524 1077 1657 2109 2572 3008 6208 6798 7379 18 527 1078 1658 2110 2573 3009 6210 6799 7380 19 532 1079 1659 2111 2574 3010 6212 6800 7381 22 534 1080 1660 2112 2575 3011 6213 6801 7382 24 535 1081 1661 2113 2576 3012 6214 6802 7384 28 536 1082 1662 2114 2577 3013 6215 6803 7386 33 537 1083 1663 2115 2578 3014 6216 6804 7387 34 538 1084 1664 2116 2579 3015 6217 6805 7388 35 539 1085 1665 2117 2580 3016 6218 6806 7389 36 540 1086 1666 2118 2581 3018 6219 6807 7390 37 541 1087 1667 2119 2582 3019 6222 6808 7391 38 542 1088 1668 2120 2583 3020 6223 6809 7392 39 543 1089 1669 2121 2584 3021 6226 6810 7393 40 544 1090 1670 2122 2585 3022 6227 6811 7394 41 545 1091 1671 2123 2586 3023 6229 6814 7396 42 546 1092 1672 2125 2587 3025 6234 6815 7397 43 547 1093 1673 2126 2588 3026 6235 6820 7398 44 548 1094 1674 2127 2589 3027 6236 6822 7400 45 549 1095 1675 2128 2590 3028 6237 6824 7402 46 550 1097 1676 2129 2591 3029 6239 6826 7403 47 553 1103 1677 2130 2592 3030 6240 6827 7404 48 554 1110 1678 2132 2593 3031 6241 6829 7406 49 555 1115 1679 2133 2594 3032 6243 6830 7409 50 556 1116 1680 2134 2595 3033 6244 6832 7412 51 557 1117 1681 2135 2596 3034 6245 6833 7413 52 558 1118 1682 2136 2597 3035 6247 6834 7414 53 559 1119 1683 2137 2598 3036 6248 6835 7415 54 560 1120 1684 2138 2599 3037 6249 6836 7416 55 561 1121 1685 2139 2600 3038 6250 6837 7417 56 562 1122 1686 2140 2601 3039 6253 6838 7418 57 563 1124 1687 2141 2602 3040 6254 6841 7419 58 564 1126 1688 2142 2603 3041 6255 6842 7420 59 565 1131 1689 2143 2604 3042 6257 6843 7424 60 566 1134 1690 2144 2605 3043 6258 6844 7426 61 567 1136 1691 2145 2606 3044 6261 6845 7427 62 568 1137 1692 2146 2607 3045 6263 6846 7428 63 570 1138 1693 2147 2608 3046 6264 6847 7430 64 571 1139 1694 2148 2610 3047 6265 6848 7431 65 572 1140 1695 2149 2611 3048 6266 6849 7432 66 575 1141 1696 2150 2612 3049 6267 6850 7433 67 581 1142 1697 2151 2613 3050 6268 6851 7434 68 583 1143 1698 2152 2614 3051 6269 6852 7435 69 584 1144 1699 2153 2615 3052 6271 6853 7436 70 585 1145 1700 2154 2616 3053 6272 6854 7438 71 587 1146 1701 2155 2617 3054 6273 6855 7441 72 589 1147 1702 2156 2618 3055 6275 6857 7442 73 590 1148 1703 2158 2619 3056 6277 6858 7443 74 591 1149 1704 2159 2620 3057 6278 6859 7444 75 592 1150 1705 2161 2621 3058 6279 6860 7445 76 593 1151 1706 2162 2622 3059 6280 6861 7446 77 594 1152 1707 2163 2623 3060 6281 6863 7448 78 595 1153 1708 2164 2624 3061 6282 6864 7449 79 596 1154 1709 2165 2625 3062 6284 6865 7450 80 597 1155 1710 2166 2626 3063 6285 6866 7451 81 598 1156 1711 2167 2627 3064 6286 6867 7452 82 599 1157 1712 2168 2628 3065 6287 6868 7453 83 600 1158 1713 2170 2629 3066 6288 6869 7455 84 601 1159 1714 2171 2630 3067 6290 6870 7457 85 602 1160 1715 2172 2631 3068 6292 6871 7458 86 604 1161 1716 2173 2632 3070 6293 6872 7461 87 605 1162 1717 2174 2633 3071 6294 6873 7462 88 606 1163 1718 2175 2634 3072 6295 6874 7464 89 607 1164 1719 2176 2635 3073 6298 6876 7466 90 610 1165 1720 2177 2636 3074 6299 6877 7467 91 611 1166 1721 2178 2637 3075 6302 6878 7469 92 614 1167 1722 2179 2638 3076 6304 6879 7470 94 616 1168 1723 2180 2639 3077 6305 6880 7471 95 617 1169 1724 2181 2640 3078 6306 6881 7472 96 618 1170 1725 2182 2641 3079 6307 6882 7473 97 624 1171 1726 2183 2642 3080 6308 6883 7474 98 625 1172 1728 2184 2643 3081 6309 6885 7475 99 626 1173 1729 2185 2644 3082 6310 6886 7476 100 628 1174 1730 2186 2645 3083 6311 6890 7477 101 631 1176 1731 2188 2646 3084 6312 6891 7479 102 632 1177 1733 2189 2647 3085 6313 6892 7483 103 633 1178 1734 2190 2648 3086 6314 6893 7484 104 634 1181 1735 2191 2649 3087 6315 6894 7485 105 636 1182 1736 2192 2650 3088 6316 6895 7488 106 640 1184 1737 2193 2651 3089 6317 6896 7489 107 645 1185 1738 2194 2652 3090 6319 6897 7491 108 647 1186 1739 2195 2653 3091 6320 6898 7492 110 648 1187 1740 2196 2654 3092 6321 6899 7493 112 649 1188 1741 2197 2655 3093 6322 6900 7494 113 650 1190 1742 2198 2656 3094 6324 6902 7495 114 652 1193 1743 2199 2657 3095 6325 6903 7496 115 653 1197 1744 2200 2658 3096 6326 6906 7497 116 654 1198 1745 2201 2659 3097 6327 6907 7499 117 655 1199 1747 2202 2660 3098 6328 6908 7500 118 656 1200 1748 2203 2661 3099 6329 6910 7501 119 657 1201 1750 2204 2662 3100 6331 6911 7502 120 659 1202 1751 2205 2663 3101 6334 6913 7503 121 660 1203 1752 2206 2664 3102 6335 6915 7505 122 661 1204 1753 2207 2665 3103 6336 6917 7507 123 662 1205 1754 2210 2666 3104 6337 6918 7508 124 663 1206 1755 2211 2667 3105 6338 6919 7509 125 664 1207 1756 2212 2668 3106 6339 6920 7510 126 666 1208 1757 2213 2669 3107 6340 6921 7511 127 667 1209 1758 2214 2670 3108 6343 6923 7512 128 668 1210 1759 2218 2671 3109 6344 6924 7513 129 669 1211 1760 2219 2672 3110 6345 6925 7514 130 670 1212 1761 2222 2673 3111 6347 6928 7515 131 673 1213 1762 2223 2674 3112 6349 6929 7516 132 677 1214 1764 2224 2675 3113 6350 6930 7517 133 678 1215 1765 2225 2676 3114 6351 6931 7518 134 679 1216 1766 2226 2677 3115 6352 6932 7519 135 680 1217 1767 2227 2678 3116 6353 6933 7520 136 681 1218 1769 2228 2679 3117 6355 6934 7521 137 684 1219 1770 2229 2680 3118 6356 6939 7523 138 687 1220 1771 2230 2681 3119 6357 6942 7525 139 689 1221 1772 2231 2682 3120 6358 6943 7526 140 690 1222 1773 2232 2683 3121 6359 6944 7528 141 692 1223 1774 2233 2684 3122 6360 6947 7529 142 694 1224 1775 2234 2685 3123 6363 6948 7530 143 700 1225 1776 2235 2686 3124 6364 6950 7532 144 702 1226 1777 2236 2687 3125 6366 6951 7534 145 706 1227 1778 2237 2688 3126 6367 6952 7535 146 711 1228 1779 2238 2689 3127 6368 6953 7536 147 715 1229 1780 2239 2690 3128 6369 6954 7537 148 716 1230 1781 2240 2691 3129 6370 6957 7538 149 717 1231 1782 2241 2692 3130 6372 6961 7540 150 719 1232 1783 2242 2693 3131 6374 6962 7541 151 720 1233 1784 2244 2694 3132 6377 6965 7542 152 724 1234 1785 2245 2695 3133 6378 6966 7545 153 726 1235 1786 2246 2696 3134 6379 6968 7547 154 727 1236 1787 2247 2697 3135 6380 6969 7548 155 729 1237 1788 2248 2698 3136 6381 6970 7549 156 731 1238 1789 2249 2699 3138 6383 6971 7550 157 738 1239 1790 2250 2700 3139 6384 6972 7555 158 739 1240 1792 2251 2701 3141 6385 6973 7556 159 740 1241 1793 2252 2702 3142 6389 6974 7558 160 745 1242 1794 2253 2703 3144 6390 6976 7560 161 747 1243 1795 2254 2704 3146 6393 6978 7561 162 755 1244 1796 2255 2708 3147 6394 6979 7562 163 756 1245 1797 2256 2709 3152 6395 6980 7563 164 759 1246 1799 2257 2710 3153 6396 6982 7564 165 765 1247 1800 2259 2711 3154 6397 6984 7565 166 766 1248 1801 2260 2712 3155 6398 6985 7566 167 767 1249 1802 2261 2713 3157 6399 6989 7567 168 768 1250 1803 2262 2714 3162 6400 6990 7568 169 769 1251 1804 2263 2715 3163 6401 6993 7569 170 770 1252 1805 2264 2716 3166 6402 6996 7570 171 771 1253 1806 2265 2717 3167 6403 6998 7574 172 772 1254 1808 2266 2718 3169 6404 6999 7575 173 773 1255 1809 2268 2719 3171 6406 7001 7576 174 774 1256 1810 2270 2720 3172 6407 7002 7579 175 775 1257 1811 2271 2721 3173 6409 7003 7580 176 776 1258 1812 2272 2722 3175 6410 7004 7581 177 780 1259 1813 2273 2723 3176 6411 7005 7582 178 781 1261 1815 2274 2724 3177 6412 7006 7585 179 782 1262 1816 2275 2725 3180 6415 7007 7586 180 783 1263 1818 2276 2726 3181 6417 7008 7587 181 784 1264 1819 2277 2727 3183 6418 7009 7588 182 785 1265 1824 2278 2728 3184 6419 7012 7590 183 789 1266 1825 2279 2729 3188 6420 7013 7591 184 790 1267 1827 2280 2730 3190 6421 7014 7592 185 794 1268 1828 2281 2731 3196 6423 7015 7595 186 797 1269 1829 2282 2732 3198 6424 7016 7596 187 798 1270 1831 2286 2733 3199 6425 7017 7597 188 799 1271 1832 2287 2734 3201 6426 7020 7599 190 800 1272 1834 2288 2735 3202 6427 7021 7600 191 801 1273 1835 2289 2736 3203 6431 7023 7603 192 802 1274 1838 2291 2737 3204 6432 7024 7606 193 803 1275 1840 2293 2738 3205 6433 7025 7607 194 804 1276 1842 2294 2739 3206 6434 7026 7610 195 805 1277 1843 2295 2740 3207 6435 7027 7612 196 806 1278 1844 2299 2741 3208 6437 7028 7613 197 807 1279 1845 2300 2742 3209 6439 7030 7615 198 808 1280 1846 2301 2743 3211 6440 7031 7620 199 809 1282 1847 2302 2744 3213 6441 7032 7621 200 810 1288 1848 2303 2745 3214 6442 7033 7622 201 811 1290 1849 2304 2746 3218 6443 7034 7624 202 812 1295 1850 2305 2747 3219 6444 7035 7625 203 813 1296 1851 2306 2748 3220 6445 7036 7626 204 814 1298 1852 2307 2750 3223 6446 7037 7627 205 815 1299 1853 2308 2751 3225 6448 7038 7628 206 816 1301 1855 2309 2752 3228 6449 7040 7629 207 817 1302 1856 2310 2753 3233 6451 7043 7631 208 818 1304 1857 2311 2754 3234 6453 7045 7632 209 819 1305 1858 2312 2755 3235 6454 7046 7633 210 820 1308 1859 2313 2756 3240 6455 7047 7634 211 821 1311 1860 2314 2757 3247 6456 7049 7635 212 822 1312 1861 2315 2758 3248 6457 7050 7636 213 823 1314 1862 2316 2759 3251 6458 7051 7638 214 824 1315 1863 2317 2760 3252 6459 7052 7643 215 825 1320 1864 2318 2761 3253 6460 7053 7644 216 826 1322 1865 2319 2762 3254 6461 7054 7645 217 827 1324 1866 2320 2763 3256 6462 7055 7646 218 828 1326 1867 2321 2764 3259 6463 7056 7649 219 829 1327 1868 2322 2765 3260 6465 7058 7650 220 830 1328 1869 2323 2766 3261 6467 7059 7651 221 831 1329 1870 2324 2767 3262 6469 7060 7652 222 832 1338 1871 2325 2768 3263 6473 7062 7653 223 833 1340 1872 2326 2769 3264 6474 7063 7654 224 834 1342 1873 2327 2770 3265 6475 7064 7656 225 835 1346 1874 2328 2771 3266 6476 7065 7657 226 836 1347 1875 2329 2772 3268 6477 7067 7658 227 837 1348 1876 2330 2773 3269 6478 7068 7659 228 839 1349 1877 2331 2774 3270 6479 7070 7660 229 840 1350 1878 2332 2775 3272 6480 7072 7662 230 841 1351 1879 2333 2776 3276 6484 7073 7663 231 842 1354 1880 2334 2778 3277 6486 7074 7665 232 843 1357 1881 2335 2779 3279 6488 7075 7666 233 844 1359 1882 2336 2780 3282 6490 7077 7667 234 845 1362 1883 2337 2781 3283 6491 7078 7668 235 846 1365 1884 2338 2782 3286 6492 7079 7669 236 847 1366 1885 2339 2783 3294 6493 7080 7670 237 848 1369 1886 2340 2784 3296 6495 7081 7674 238 849 1370 1887 2341 2785 3298 6496 7082 7675 239 850 1371 1888 2342 2786 3299 6497 7083 7676 240 852 1372 1889 2343 2787 3300 6499 7084 7677 241 853 1373 1890 2344 2788 3302 6501 7085 7678 242 854 1374 1891 2345 2789 3303 6502 7087 7679 243 855 1375 1892 2346 2790 3305 6503 7088 7681 244 856 1376 1893 2347 2791 3306 6505 7089 7682 245 857 1377 1894 2348 2792 3310 6506 7090 7685 246 860 1378 1895 2349 2793 3313 6507 7091 7686 247 861 1379 1896 2350 2794 3315 6509 7092 7689 248 862 1380 1897 2351 2795 3316 6510 7093 7693 249 863 1381 1898 2352 2796 3318 6511 7095 7694 250 866 1382 1899 2353 2797 3323 6512 7096 7695 251 867 1383 1900 2354 2798 3326 6515 7097 7698 252 868 1384 1901 2355 2799 3329 6522 7098 7700 253 869 1385 1902 2356 2800 4501 6524 7099 7701 254 870 1386 1903 2357 2801 4502 6525 7100 7702 255 871 1387 1904 2358 2802 4503 6526 7103 7705 256 872 1388 1905 2359 2803 4504 6527 7104 7706 257 873 1389 1906 2360 2804 4505 6529 7105 7707 258 874 1390 1907 2361 2805 4506 6530 7106 7708 259 875 1391 1908 2362 2806 4507 6531 7109 7713 261 876 1392 1909 2363 2807 4508 6532 7110 7715 262 877 1393 1910 2364 2808 4509 6533 7111 7717 263 878 1394 1911 2365 2809 4510 6535 7112 7718 264 879 1395 1912 2366 2810 4511 6538 7114 7719 265 880 1396 1913 2367 2811 4512 6540 7115 7720 266 881 1397 1914 2368 2812 4513 6541 7116 7721 267 882 1398 1915 2369 2813 4514 6542 7118 7722 268 883 1399 1916 2370 2814 4515 6543 7119 7723 269 884 1400 1917 2371 2815 4516 6544 7120 7724 270 885 1401 1918 2372 2816 4517 6545 7121 7726 271 886 1402 1919 2373 2817 4518 6547 7123 7727 272 887 1403 1920 2374 2818 4519 6548 7125 7728 273 888 1404 1921 2375 2819 4520 6549 7127 7729 274 889 1405 1922 2376 2820 4521 6551 7128 7730 275 890 1406 1923 2377 2821 4522 6552 7129 7731 276 891 1407 1924 2378 2822 4523 6554 7131 7732 277 892 1408 1925 2379 2823 4524 6555 7133 7733 278 893 1409 1926 2380 2824 4525 6557 7134 7734 279 894 1410 1927 2381 2825 4526 6559 7135 7735 280 895 1411 1928 2382 2826 4527 6561 7136 7737 281 896 1412 1929 2383 2827 4528 6563 7140 7738 283 897 1413 1931 2384 2828 4529 6564 7141 7739 284 898 1414 1932 2385 2829 4530 6565 7142 7740 285 899 1415 1933 2386 2830 4531 6566 7143 7741 286 900 1416 1934 2387 2831 4532 6567 7144 287 901 1417 1935 2388 2832 4533 6568 7147 290 902 1418 1936 2389 2833 4534 6569 7148 293 903 1419 1937 2390 2834 4535 6572 7149 294 904 1420 1938 2391 2835 4536 6573 7150 295 905 1421 1939 2392 2836 4537 6575 7151 296 906 1422 1940 2393 2837 4538 6577 7152 297 907 1423 1941 2394 2838 4539 6579 7153 298 908 1424 1942 2395 2839 4540 6580 7154 299 909 1425 1943 2396 2840 4541 6581 7155 300 910 1426 1944 2397 2841 6001 6582 7156 301 911 1427 1945 2398 2842 6004 6583 7158 302 912 1428 1946 2399 2843 6006 6584 7159 303 913 1429 1947 2400 2844 6007 6585 7160 304 914 1430 1948 2401 2845 6008 6586 7161 305 915 1431 1949 2402 2846 6010 6587 7162 306 916 1432 1950 2403 2847 6011 6588 7163 307 917 1433 1951 2404 2848 6012 6589 7164 308 918 1434 1952 2405 2849 6013 6590 7166 309 919 1435 1953 2406 2850 6014 6591 7167 310 920 1436 1954 2407 2851 6015 6593 7168 312 921 1437 1955 2408 2852 6017 6594 7169 313 922 1439 1956 2409 2853 6018 6595 7170 314 923 1440 1957 2410 2854 6019 6596 7171 315 924 1441 1958 2411 2855 6021 6597 7172 316 925 1442 1959 2412 2856 6022 6598 7174 317 926 1443 1960 2413 2857 6023 6599 7175 318 927 1444 1961 2414 2858 6024 6600 7176 319 928 1445 1962 2415 2859 6025 6601 7177 320 929 1446 1963 2416 2860 6026 6602 7179 321 930 1447 1964 2417 2861 6028 6603 7180 322 931 1448 1965 2418 2862 6029 6605 7181 323 932 1449 1966 2419 2863 6030 6606 7183 324 933 1450 1967 2420 2864 6031 6607 7184 325 934 1451 1968 2422 2865 6033 6608 7186 326 936 1452 1969 2423 2866 6035 6609 7187 327 937 1455 1970 2424 2867 6036 6610 7188 328 938 1456 1971 2425 2868 6038 6611 7191 329 939 1460 1972 2426 2869 6040 6612 7192 330 940 1462 1973 2427 2870 6041 6613 7194 331 941 1471 1974 2431 2871 6043 6614 7195 332 942 1473 1975 2436 2872 6045 6615 7196 333 943 1475 1976 2438 2873 6046 6617 7197 334 944 1488 1977 2440 2874 6048 6618 7198 335 945 1489 1978 2441 2875 6049 6619 7201 336 946 1491 1979 2442 2876 6050 6621 7203 337 948 1492 1980 2443 2877 6051 6622 7204 338 950 1493 1981 2444 2878 6054 6623 7206 339 951 1497 1982 2445 2880 6055 6624 7208 340 952 1499 1983 2446 2881 6056 6625 7209 341 957 1504 1984 2447 2882 6057 6627 7210 342 958 1505 1985 2448 2884 6058 6628 7212 343 959 1506 1986 2449 2885 6059 6629 7214 344 960 1507 1987 2450 2886 6060 6630 7215 345 961 1508 1988 2451 2887 6061 6632 7216 346 962 1510 1989 2452 2888 6063 6635 7217 347 963 1513 1990 2453 2889 6064 6637 7218 348 964 1515 1991 2454 2890 6066 6639 7220 349 965 1519 1992 2455 2891 6067 6642 7221 350 966 1521 1993 2456 2892 6068 6644 7222 351 967 1523 1994 2457 2893 6069 6645 7223 352 968 1524 1995 2458 2894 6071 6646 7226 353 969 1527 1996 2459 2895 6072 6648 7227 354 970 1529 1997 2460 2896 6073 6650 7228 355 971 1531 1998 2461 2897 6074 6651 7230 356 972 1539 1999 2462 2898 6075 6652 7231 357 973 1540 2000 2463 2899 6076 6654 7232 358 974 1541 2001 2464 2900 6079 6655 7233 359 975 1542 2002 2465 2901 6080 6656 7235 360 976 1543 2003 2466 2902 6081 6659 7236 361 977 1544 2004 2467 2903 6082 6661 7237 362 978 1545 2005 2468 2904 6083 6664 7238 363 979 1546 2006 2469 2905 6084 6665 7239 364 980 1547 2007 2470 2906 6085 6666 7240 365 981 1548 2008 2471 2907 6088 6669 7242 366 982 1549 2009 2472 2908 6089 6671 7243 367 983 1550 2010 2473 2909 6090 6672 7244 368 984 1551 2011 2474 2910 6091 6674 7246 369 985 1552 2012 2476 2911 6092 6675 7247 370 986 1553 2013 2477 2912 6093 6676 7250 371 987 1554 2014 2478 2913 6094 6679 7251 372 988 1555 2015 2479 2914 6096 6680 7252 373 989 1556 2016 2480 2915 6097 6681 7253 374 990 1557 2017 2481 2916 6099 6683 7255 375 991 1558 2018 2482 2917 6101 6684 7258 376 992 1559 2019 2483 2918 6102 6685 7260 377 993 1560 2020 2484 2919 6103 6686 7261 379 994 1561 2021 2485 2920 6105 6687 7262 380 996 1563 2022 2488 2921 6106 6688 7263 381 997 1564 2023 2489 2922 6107 6689 7264 382 999 1565 2024 2490 2923 6108 6690 7265 383 1000 1566 2025 2491 2924 6109 6691 7266 384 1001 1567 2026 2492 2925 6110 6692 7267 385 1003 1568 2027 2497 2926 6112 6693 7270 386 1004 1570 2028 2498 2927 6115 6694 7273 387 1006 1571 2029 2501 2928 6116 6695 7274 388 1007 1572 2030 2502 2929 6117 6698 7275 389 1008 1573 2031 2503 2930 6118 6703 7276 390 1009 1574 2032 2504 2931 6121 6705 7278 391 1010 1575 2033 2505 2932 6122 6706 7281 392 1011 1576 2034 2506 2933 6123 6708 7282 393 1012 1577 2035 2507 2934 6124 6709 7284 394 1013 1578 2036 2508 2935 6125 6713 7286 395 1014 1579 2037 2509 2936 6129 6715 7288 396 1015 1580 2038 2510 2937 6130 6716 7289 397 1016 1581 2039 2511 2938 6131 6717 7291 398 1017 1582 2040 2512 2939 6133 6718 7292 399 1018 1583 2041 2513 2940 6136 6719 7293 400 1019 1584 2042 2514 2941 6137 6720 7294 401 1020 1585 2043 2515 2942 6138 6722 7297 402 1021 1587 2044 2516 2943 6139 6723 7298 403 1022 1588 2045 2517 2944 6140 6724 7299 404 1023 1590 2046 2518 2945 6141 6726 7301 405 1024 1592 2047 2519 2946 6142 6728 7302 406 1025 1593 2048 2520 2947 6143 6730 7303 407 1026 1594 2049 2521 2948 6144 6731 7304 408 1027 1597 2050 2522 2949 6147 6732 7305 409 1028 1598 2051 2523 2950 6148 6733 7306 410 1029 1599 2052 2524 2951 6150 6734 7307 413 1030 1600 2053 2525 2952 6151 6736 7309 415 1031 1604 2054 2526 2953 6152 6738 7311 416 1032 1605 2055 2527 2954 6153 6739 7312 419 1033 1606 2056 2528 2955 6154 6740 7313 420 1034 1607 2057 2529 2957 6155 6741 7315 421 1035 1608 2058 2530 2958 6157 6743 7317 424 1036 1610 2059 2531 2959 6158 6744 7320 426 1037 1611 2060 2532 2960 6159 6745 7322 427 1038 1612 2061 2533 2962 6160 6746 7323 428 1039 1616 2062 2534 2965 6164 6747 7326 429 1040 1617 2063 2535 2966 6165 6750 7327 432 1041 1618 2064 2536 2967 6167 6751 7328 433 1042 1619 2066 2537 2968 6168 6752 7329 437 1043 1620 2069 2538 2969 6169 6754 7331 438 1044 1621 2070 2539 2971 6171 6756 7332 441 1045 1622 2071 2540 2972 6172 6757 7335 443 1046 1623 2072 2541 2973 6173 6758 7336 446 1047 1624 2074 2542 2974 6174 6760 7337 449 1048 1625 2075 2543 2975 6175 6761 7339 450 1049 1626 2076 2544 2976 6176 6762 7340 452 1050 1627 2079 2545 2978 6177 6764 7342 460 1051 1628 2080 2546 2979 6178 6765 7343 461 1052 1629 2081 2547 2981 6179 6771 7344 462 1053 1630 2082 2548 2982 6180 6772 7345 464 1054 1631 2084 2549 2983 6181 6773 7346 465 1055 1632 2085 2550 2984 6182 6774 7347 469 1056 1633 2086 2551 2985 6183 6775 7348 470 1057 1634 2089 2552 2986 6184 6776 7349 472 1058 1635 2090 2553 2987 6185 6777 7350 475 1059 1636 2091 2554 2988 6186 6778 7351 476 1060 1637 2092 2555 2989 6187 6779 7352 480 1061 1638 2093 2556 2990 6188 6780 7354 481 1062 1639 2094 2557 2991 6189 6781 7357 483 1063 1640 2095 2558 2992 6190 6782 7358 484 1064 1641 2096 2559 2993 6191 6783 7360

To characterize the reproducibility of the selected candidates without cell-type and test template confounders, two additional full experimental replicates were executed for the test template g4 condition in HEK293T cells (herein conditions 1b and 1c; original condition 1 hereafter became condition 1a) following the same experimental procedures detailed above. The analysis of the three condition 1 replicates identified a subset of approximately 260 gene modifying polypeptide candidates having a Z score of at least 1 or greater across all of replicates 1a, 1b, and 1c. These results show that this subset of gene modifying polypeptides had reproducible editing activity in all condition 1 replicates of the screening assay under this revised analysis. These include gene modifying polypeptides having amino acid sequences according to any one of the SEQ ID NOs listed in Table D7 below.

TABLE D7 Gene modifying polypeptide candidates having a Z-score of at least 1 or greater across all of replicates 1a, 1b, and 1c. SEQ ID NOs 156 1376 2320 2678 2927 4511 6760 300 1401 2324 2700 2929 4512 6761 317 1423 2327 2701 2930 4513 6783 346 1441 2329 2711 2933 4514 6788 352 1553 2331 2712 2937 4515 6876 591 1860 2332 2737 2953 4516 6883 647 1863 2333 2741 2957 4517 6998 801 1867 2338 2748 2972 4518 7067 871 1871 2343 2760 2983 4520 7103 898 1874 2345 2772 2995 4522 7121 933 1875 2359 2780 3007 4523 7142 1007 1876 2360 2781 3039 4524 7154 1008 1939 2370 2784 3044 4525 7242 1009 1943 2382 2786 3045 4526 7262 1011 1949 2400 2787 3057 4527 7267 1018 1951 2405 2788 3063 4528 7293 1021 1967 2510 2790 3065 4529 7335 1029 2060 2514 2791 3067 4530 7443 1033 2086 2527 2795 3076 4531 7476 1034 2092 2529 2797 3079 4533 7496 1037 2094 2535 2800 3083 4534 7509 1039 2104 2536 2810 3084 4535 7555 1044 2112 2539 2815 3085 4536 7587 1046 2114 2550 2820 3093 4537 7588 1047 2117 2553 2823 3096 4538 7660 1052 2132 2573 2825 3099 4539 7667 1056 2145 2583 2826 3103 4540 1059 2148 2599 2830 3107 4541 1060 2149 2610 2835 3111 6030 1076 2161 2615 2836 3123 6073 1083 2165 2620 2850 4501 6091 1093 2172 2631 2880 4502 6181 1197 2174 2634 2881 4503 6402 1198 2196 2636 2888 4504 6434 1219 2249 2644 2893 4506 6505 1242 2280 2654 2903 4507 6567 1262 2301 2656 2913 4508 6568 1372 2311 2657 2914 4509 6591 1373 2313 2660 2916 4510 6738

Approximately 3070 gene modifying polypeptide candidates within the library had a Z-score of at least 1 or greater in any one of conditions 1a, 1b, or 1c using this further analysis. These results show that this subset of gene modifying polypeptides had editing activity in at least one replicate of condition 1 of the screening assay under this revised analysis. The subset of these gene modifying polypeptides are encoded by amino acid sequences of any one of the SEQ ID NOs listed in Table D8 below.

TABLE D8 Gene modifying polypeptide candidates having a Z-score of at least 1 or greater in any one of conditions 1a, 1b, or 1c. SEQ ID NOs 1 731 1242 1882 2326 2690 3059 6301 6729 7174 7620 34 746 1243 1883 2327 2691 3060 6303 6730 7176 7621 35 765 1244 1884 2328 2692 3061 6304 6731 7178 7623 36 770 1245 1885 2329 2695 3062 6305 6732 7179 7625 37 772 1246 1886 2330 2697 3063 6307 6733 7180 7626 38 777 1247 1887 2331 2699 3064 6308 6734 7182 7627 39 780 1250 1889 2332 2700 3065 6310 6735 7183 7629 40 799 1253 1890 2333 2701 3066 6311 6737 7184 7630 45 800 1254 1891 2334 2702 3067 6312 6738 7185 7632 46 801 1255 1892 2335 2703 3068 6313 6742 7186 7633 47 802 1256 1893 2336 2711 3069 6314 6744 7187 7634 48 803 1257 1894 2337 2712 3070 6315 6746 7190 7635 49 804 1258 1896 2338 2713 3071 6316 6748 7191 7636 50 805 1259 1898 2339 2714 3072 6317 6749 7192 7637 51 806 1260 1899 2340 2715 3073 6320 6751 7194 7638 52 807 1261 1900 2341 2716 3074 6322 6752 7195 7639 55 808 1262 1901 2342 2717 3075 6324 6753 7196 7640 56 809 1263 1903 2343 2718 3076 6325 6754 7197 7641 57 811 1264 1905 2344 2719 3077 6327 6755 7198 7642 59 812 1265 1906 2345 2720 3078 6328 6758 7199 7643 61 813 1266 1907 2346 2721 3079 6329 6759 7200 7644 62 814 1267 1908 2347 2722 3080 6330 6760 7201 7646 63 817 1268 1909 2348 2723 3081 6332 6761 7202 7647 64 818 1269 1912 2349 2724 3082 6333 6763 7203 7648 65 819 1270 1913 2350 2726 3083 6336 6765 7204 7649 67 820 1272 1915 2351 2727 3084 6339 6766 7206 7650 68 821 1273 1916 2352 2728 3085 6340 6767 7209 7651 69 824 1274 1917 2353 2729 3086 6341 6768 7211 7653 70 825 1276 1918 2354 2730 3087 6342 6769 7212 7654 71 827 1278 1920 2355 2731 3088 6343 6772 7213 7655 72 828 1279 1921 2356 2732 3090 6344 6773 7216 7656 76 829 1281 1922 2357 2734 3091 6348 6774 7219 7658 78 830 1288 1923 2358 2736 3093 6349 6776 7222 7660 79 833 1298 1924 2359 2737 3094 6351 6777 7224 7661 81 834 1311 1925 2360 2739 3095 6352 6778 7225 7662 83 835 1319 1926 2361 2740 3096 6354 6780 7226 7664 85 836 1330 1927 2362 2741 3097 6355 6781 7227 7665 86 837 1343 1929 2363 2742 3098 6356 6782 7229 7666 88 839 1346 1932 2364 2743 3099 6357 6783 7230 7667 89 843 1348 1934 2365 2744 3100 6359 6784 7232 7670 90 844 1353 1935 2366 2745 3101 6360 6785 7234 7671 93 847 1354 1936 2367 2746 3102 6361 6786 7235 7672 94 848 1370 1937 2368 2747 3103 6362 6788 7240 7673 96 849 1371 1938 2369 2748 3104 6363 6789 7241 7675 97 850 1372 1939 2370 2750 3105 6364 6790 7242 7676 100 851 1373 1940 2371 2751 3106 6365 6793 7244 7678 103 852 1374 1941 2372 2753 3107 6366 6796 7245 7679 106 853 1375 1942 2373 2754 3108 6367 6797 7246 7680 108 854 1376 1943 2374 2755 3109 6368 6798 7248 7682 110 861 1377 1944 2375 2758 3110 6370 6801 7249 7683 111 862 1379 1945 2376 2760 3111 6371 6802 7250 7684 114 863 1380 1946 2377 2761 3112 6372 6803 7253 7687 115 866 1381 1947 2378 2764 3113 6373 6804 7254 7688 116 867 1383 1948 2379 2768 3114 6374 6808 7256 7689 117 870 1384 1949 2380 2769 3116 6375 6809 7257 7690 118 871 1385 1950 2381 2772 3117 6376 6810 7258 7691 119 872 1386 1951 2382 2773 3118 6377 6811 7259 7692 120 873 1387 1952 2383 2775 3119 6380 6812 7260 7693 121 874 1388 1953 2384 2776 3120 6381 6813 7261 7694 122 876 1389 1954 2385 2777 3121 6382 6815 7262 7695 123 877 1390 1955 2386 2780 3122 6383 6816 7263 7696 124 878 1391 1956 2387 2781 3123 6385 6817 7264 7697 125 879 1393 1957 2388 2782 3124 6386 6818 7266 7698 126 880 1394 1958 2389 2783 3125 6387 6819 7267 7699 127 881 1395 1959 2390 2784 3126 6388 6820 7268 7701 130 883 1396 1960 2391 2785 3127 6390 6821 7269 7702 131 884 1397 1961 2392 2786 3128 6391 6822 7271 7703 134 885 1398 1962 2393 2787 3129 6392 6825 7272 7704 137 886 1399 1964 2394 2788 3130 6394 6828 7273 7706 138 887 1400 1965 2395 2789 3131 6395 6829 7274 7707 139 888 1401 1966 2396 2790 3133 6402 6831 7275 7709 143 890 1402 1967 2397 2791 3134 6405 6833 7276 7710 144 891 1403 1968 2398 2792 3135 6407 6835 7277 7711 145 892 1404 1969 2399 2793 3136 6408 6837 7279 7712 146 893 1405 1970 2400 2794 3194 6409 6839 7281 7716 147 894 1406 1972 2401 2795 3231 6410 6840 7282 7717 150 897 1408 1973 2402 2796 3317 6412 6844 7283 7719 153 898 1409 1974 2403 2797 4501 6413 6845 7284 7725 154 899 1410 1975 2404 2798 4502 6414 6846 7285 7728 156 900 1411 1976 2405 2799 4503 6416 6847 7286 7730 157 901 1412 1977 2406 2800 4504 6417 6850 7287 7736 158 902 1414 1978 2407 2801 4505 6419 6852 7291 7740 159 903 1415 1979 2408 2802 4506 6421 6855 7292 7742 160 905 1416 1980 2409 2803 4507 6422 6856 7293 7743 161 907 1417 1981 2410 2804 4508 6424 6858 7294 162 908 1418 1982 2412 2805 4509 6425 6859 7295 163 909 1419 1983 2413 2806 4510 6426 6861 7298 164 910 1420 1984 2414 2807 4511 6428 6862 7299 165 912 1422 1985 2415 2808 4512 6429 6863 7300 167 914 1423 1986 2416 2809 4513 6430 6864 7301 168 915 1424 1987 2440 2810 4514 6431 6866 7302 170 916 1425 1988 2443 2811 4515 6432 6867 7303 171 917 1426 1989 2444 2812 4516 6434 6868 7305 172 918 1427 1990 2447 2813 4517 6436 6869 7306 174 919 1428 1991 2448 2814 4518 6438 6870 7308 176 920 1430 1992 2449 2815 4519 6439 6872 7309 177 921 1433 1993 2451 2816 4520 6440 6874 7310 180 922 1434 1994 2452 2817 4521 6441 6875 7311 181 923 1437 1995 2453 2818 4522 6443 6876 7312 182 924 1439 1996 2454 2820 4523 6444 6878 7313 184 925 1440 1998 2455 2821 4524 6445 6883 7316 190 928 1441 1999 2456 2822 4525 6447 6885 7317 191 929 1442 2000 2457 2823 4526 6450 6886 7318 192 933 1443 2002 2458 2824 4527 6452 6888 7319 195 934 1444 2003 2459 2825 4528 6455 6889 7320 196 935 1445 2004 2460 2826 4529 6458 6890 7321 199 936 1446 2006 2461 2827 4530 6464 6891 7322 200 938 1447 2009 2462 2828 4531 6465 6892 7323 203 940 1448 2010 2465 2829 4532 6466 6896 7324 204 942 1454 2011 2466 2830 4533 6467 6897 7325 206 943 1460 2012 2467 2831 4534 6468 6898 7326 208 944 1465 2013 2469 2832 4535 6469 6902 7329 209 946 1469 2014 2470 2833 4536 6470 6906 7330 210 947 1475 2016 2471 2834 4537 6471 6908 7333 213 948 1504 2017 2480 2835 4538 6472 6909 7334 215 951 1542 2018 2481 2836 4539 6476 6910 7335 216 959 1543 2020 2483 2837 4540 6477 6911 7336 217 960 1544 2023 2485 2838 4541 6478 6912 7338 218 961 1546 2024 2486 2839 6001 6479 6914 7339 219 962 1547 2025 2488 2840 6002 6480 6915 7341 220 963 1549 2027 2489 2841 6003 6481 6916 7342 222 964 1550 2028 2496 2842 6005 6482 6919 7343 223 965 1552 2029 2502 2843 6008 6483 6920 7345 224 966 1553 2030 2503 2844 6009 6485 6922 7346 225 967 1556 2031 2504 2845 6010 6486 6923 7348 226 968 1565 2033 2505 2846 6012 6487 6924 7349 227 969 1566 2034 2506 2847 6013 6488 6925 7351 229 970 1567 2035 2507 2848 6014 6489 6926 7352 231 971 1568 2036 2508 2849 6016 6491 6927 7353 232 972 1570 2037 2509 2850 6020 6493 6928 7355 234 975 1573 2041 2510 2851 6022 6494 6930 7356 236 976 1576 2043 2511 2852 6027 6498 6931 7357 237 977 1577 2045 2512 2853 6028 6499 6933 7358 238 978 1579 2047 2513 2854 6029 6500 6935 7359 239 979 1580 2048 2514 2856 6030 6501 6936 7360 240 980 1584 2050 2515 2857 6032 6502 6937 7363 241 981 1585 2051 2516 2858 6034 6503 6938 7364 248 982 1588 2052 2517 2859 6036 6504 6939 7365 252 983 1590 2055 2518 2860 6037 6505 6940 7366 253 985 1593 2060 2519 2861 6038 6508 6941 7367 254 986 1595 2071 2520 2862 6039 6509 6942 7368 255 987 1596 2072 2521 2863 6041 6511 6943 7369 257 988 1599 2084 2522 2864 6042 6512 6945 7370 258 989 1616 2086 2523 2865 6043 6513 6946 7371 259 990 1617 2087 2524 2866 6044 6514 6948 7372 260 993 1618 2088 2525 2867 6045 6515 6949 7373 261 994 1619 2089 2526 2868 6047 6516 6952 7376 262 995 1620 2091 2527 2869 6048 6517 6954 7378 265 996 1621 2092 2528 2870 6049 6518 6955 7381 266 998 1622 2093 2529 2871 6052 6519 6956 7384 267 999 1625 2094 2530 2872 6053 6521 6957 7385 268 1001 1628 2096 2531 2873 6054 6522 6958 7387 269 1002 1629 2100 2532 2874 6057 6523 6959 7389 270 1003 1632 2101 2533 2875 6059 6524 6960 7393 271 1005 1633 2102 2534 2877 6062 6525 6961 7394 272 1006 1634 2103 2535 2878 6063 6526 6963 7395 273 1007 1635 2104 2536 2880 6065 6527 6964 7397 283 1008 1636 2107 2537 2881 6067 6528 6966 7399 284 1009 1638 2108 2538 2882 6070 6530 6967 7400 286 1010 1639 2109 2539 2883 6071 6531 6968 7401 287 1011 1640 2111 2540 2884 6073 6532 6969 7402 288 1012 1644 2112 2541 2885 6074 6534 6973 7403 292 1014 1646 2114 2542 2886 6077 6536 6975 7405 295 1015 1652 2115 2543 2887 6078 6537 6977 7407 297 1016 1655 2116 2544 2888 6079 6539 6979 7408 298 1017 1659 2117 2545 2890 6082 6540 6980 7410 300 1018 1660 2121 2546 2891 6083 6542 6981 7411 301 1019 1662 2124 2547 2893 6084 6543 6982 7412 302 1020 1663 2125 2548 2894 6086 6546 6983 7416 304 1021 1664 2126 2549 2895 6087 6549 6985 7417 305 1022 1665 2128 2550 2896 6091 6550 6986 7418 306 1023 1666 2131 2551 2897 6093 6551 6987 7421 307 1024 1667 2132 2552 2898 6095 6552 6988 7422 309 1025 1669 2133 2553 2899 6097 6553 6989 7423 310 1027 1670 2135 2554 2900 6098 6555 6990 7424 312 1028 1671 2136 2555 2901 6100 6556 6991 7425 313 1029 1672 2137 2556 2903 6104 6558 6992 7429 314 1030 1673 2142 2557 2904 6105 6559 6993 7430 315 1031 1675 2143 2558 2905 6106 6560 6994 7433 317 1032 1679 2144 2559 2906 6108 6561 6995 7435 318 1033 1680 2145 2560 2907 6111 6562 6997 7436 319 1034 1681 2146 2561 2908 6113 6564 6998 7437 320 1035 1682 2147 2562 2909 6114 6566 7000 7439 321 1037 1686 2148 2563 2911 6115 6567 7003 7440 322 1038 1687 2149 2564 2912 6117 6568 7005 7443 323 1039 1688 2153 2565 2913 6118 6570 7008 7444 324 1040 1689 2157 2566 2914 6119 6571 7009 7447 326 1041 1690 2158 2567 2916 6120 6572 7010 7453 328 1042 1691 2159 2568 2917 6121 6574 7011 7454 329 1043 1694 2160 2569 2918 6123 6575 7012 7456 330 1044 1695 2161 2570 2919 6126 6576 7013 7459 331 1045 1698 2165 2571 2920 6127 6578 7014 7460 332 1046 1699 2166 2572 2921 6128 6579 7015 7462 334 1047 1700 2167 2573 2922 6129 6581 7017 7463 335 1049 1701 2168 2574 2924 6130 6582 7018 7465 336 1050 1702 2169 2575 2925 6132 6584 7019 7468 337 1051 1704 2171 2576 2926 6133 6585 7022 7469 339 1052 1705 2172 2577 2927 6134 6587 7023 7470 343 1053 1706 2174 2578 2928 6135 6588 7024 7473 344 1054 1707 2175 2579 2929 6141 6591 7029 7474 345 1055 1708 2176 2580 2930 6142 6592 7031 7476 346 1056 1709 2177 2582 2931 6143 6594 7032 7477 347 1057 1711 2178 2583 2932 6144 6595 7033 7478 348 1058 1713 2179 2584 2933 6145 6599 7036 7480 350 1059 1714 2180 2585 2935 6146 6601 7038 7481 351 1060 1716 2187 2586 2936 6147 6603 7039 7482 352 1061 1717 2189 2587 2937 6148 6604 7041 7485 354 1062 1719 2192 2588 2938 6149 6607 7042 7486 355 1063 1720 2193 2589 2940 6150 6609 7044 7487 356 1064 1721 2194 2590 2942 6151 6610 7045 7488 357 1065 1722 2196 2591 2943 6152 6613 7046 7490 360 1066 1724 2199 2592 2944 6155 6615 7047 7493 361 1068 1726 2201 2593 2945 6156 6617 7050 7496 362 1069 1727 2204 2594 2948 6161 6618 7051 7497 363 1070 1733 2208 2595 2949 6162 6619 7054 7498 364 1071 1734 2209 2596 2950 6166 6620 7055 7499 366 1072 1735 2213 2598 2951 6169 6621 7057 7500 368 1074 1736 2214 2599 2952 6170 6622 7058 7504 369 1075 1737 2215 2600 2953 6171 6623 7059 7506 370 1076 1738 2220 2601 2954 6175 6624 7060 7507 372 1077 1740 2222 2602 2955 6176 6625 7061 7508 374 1078 1741 2223 2603 2957 6177 6626 7062 7509 375 1079 1742 2224 2605 2965 6180 6627 7064 7510 376 1080 1743 2225 2606 2966 6181 6630 7065 7513 377 1081 1744 2226 2607 2967 6182 6631 7066 7516 382 1082 1746 2227 2608 2969 6183 6632 7067 7519 384 1083 1747 2228 2610 2970 6189 6633 7068 7520 386 1084 1748 2230 2611 2971 6190 6634 7069 7522 388 1085 1751 2231 2612 2972 6194 6636 7070 7523 389 1086 1752 2232 2614 2973 6196 6638 7072 7524 390 1088 1754 2233 2615 2974 6198 6639 7073 7525 391 1089 1756 2235 2616 2975 6199 6640 7075 7526 392 1091 1759 2236 2617 2976 6200 6641 7076 7530 393 1092 1764 2237 2618 2977 6202 6642 7079 7531 394 1093 1765 2239 2619 2978 6203 6643 7080 7532 395 1096 1767 2241 2620 2981 6205 6644 7082 7533 397 1115 1768 2243 2621 2982 6206 6645 7084 7535 398 1116 1769 2244 2622 2983 6208 6646 7085 7536 399 1118 1770 2245 2623 2984 6209 6647 7086 7537 403 1127 1771 2246 2624 2985 6211 6648 7087 7538 404 1129 1772 2247 2625 2987 6213 6649 7088 7541 405 1137 1773 2248 2626 2989 6216 6650 7089 7544 406 1138 1774 2249 2627 2990 6219 6651 7091 7545 407 1143 1777 2250 2628 2991 6220 6652 7092 7546 413 1145 1778 2252 2629 2992 6221 6653 7093 7547 460 1150 1780 2253 2630 2994 6224 6654 7094 7548 474 1154 1781 2255 2631 2995 6225 6657 7095 7550 480 1155 1782 2256 2632 2996 6228 6658 7096 7551 489 1156 1785 2257 2633 2997 6229 6659 7100 7552 498 1157 1786 2260 2634 2998 6230 6660 7101 7553 517 1159 1789 2261 2635 2999 6231 6662 7102 7554 519 1161 1790 2262 2636 3002 6232 6663 7103 7555 524 1163 1791 2263 2637 3005 6233 6664 7104 7556 528 1164 1793 2265 2638 3006 6234 6666 7105 7557 534 1168 1794 2266 2639 3007 6235 6667 7106 7558 536 1169 1796 2270 2640 3008 6237 6670 7107 7559 541 1170 1799 2271 2641 3009 5238 6673 7108 7560 550 1171 1800 2272 2642 3010 6242 6674 7110 7562 555 1172 1801 2273 2643 3011 6246 6675 7111 7567 556 1176 1802 2275 2644 3012 6247 6676 7113 7569 564 1193 1804 2276 2645 3013 6248 6677 7117 7570 568 1195 1805 2278 2646 3014 6251 6678 7120 7571 569 1196 1810 2280 2647 3015 6252 6679 7121 7572 571 1197 1811 2281 2648 3018 6253 6682 7122 7573 580 1198 1812 2282 2649 3019 6256 6683 7124 7574 581 1199 1813 2283 2650 3020 6257 6684 7126 7575 586 1200 1816 2286 2651 3021 6258 6685 7127 7576 587 1201 1823 2287 2652 3022 6259 6686 7129 7577 588 1202 1824 2289 2653 3024 6260 6687 7130 7578 590 1203 1827 2291 2654 3025 6262 6688 7131 7582 591 1204 1829 2294 2655 3026 6263 6690 7132 7583 592 1205 1831 2295 2656 3027 6265 6691 7134 7584 593 1206 1835 2299 2657 3028 6267 6692 7135 7585 594 1207 1854 2300 2658 3030 6268 6695 7137 7586 595 1208 1855 2301 2659 3031 6269 6696 7139 7587 599 1209 1856 2302 2660 3035 6270 6697 7141 7588 602 1210 1857 2303 2661 3036 6271 6698 7142 7590 603 1212 1858 2304 2662 3037 6272 6699 7144 7592 611 1213 1859 2305 2663 3038 6273 6700 7145 7594 613 1214 1860 2306 2664 3039 6274 6701 7146 7596 616 1215 1861 2307 2665 3040 6275 6702 7147 7597 628 1216 1862 2308 2666 3041 6276 6704 7148 7598 638 1217 1863 2309 2667 3042 6278 6706 7149 7599 645 1218 1864 2310 2670 3043 6279 6707 7150 7600 647 1219 1865 2311 2672 3044 6280 6708 7151 7601 648 1220 1866 2312 2673 3045 6282 6709 7152 7602 649 1222 1867 2313 2674 3046 6283 6711 7153 7603 651 1223 1868 2314 2675 3047 6284 6712 7154 7604 654 1224 1869 2315 2676 3048 6285 6714 7155 7605 659 1225 1870 2316 2677 3049 6286 6715 7156 7606 660 1227 1871 2317 2678 3050 6287 6716 7158 7608 662 1228 1872 2318 2679 3051 6288 6717 7159 7609 674 1230 1874 2319 2681 3052 6290 6719 7160 7610 675 1232 1875 2320 2684 3053 6291 6720 7164 7611 676 1233 1876 2321 2685 3054 6293 6721 7165 7614 677 1235 1877 2322 2686 3055 6294 6725 7169 7615 681 1237 1878 2323 2687 3056 6296 6726 7171 7616 704 1238 1880 2324 2688 3057 6297 6727 7172 7618 722 1239 1881 2325 2689 3058 6299 6728 7173 7619

Taken together, the various analyses identified approximately 625 gene modifying polypeptides within the library that had a Z-score of at least 1 or greater in 3 or more conditions or replicates tested, and approximately 4625 gene modifying polypeptides within the library that had a Z-score of at least 1 or greater in at least one condition (these include gene modifying polypeptides having amino amino acid sequences according to any one of the SEQ ID NOs listed in Tables D9 and D10, respectively).

TABLE D9 Gene modifying polypeptide candidates having a Z-score of at least 1 or greater in 3 or more conditions or replicates tested. SEQ ID NOs 34 883 1376 1942 2332 2619 2817 3076 6567 35 884 1377 1943 2333 2620 2818 3079 6568 36 890 1380 1945 2335 2622 2820 3083 6591 37 898 1381 1949 2338 2623 2822 3084 6738 38 900 1382 1951 2342 2624 2823 3085 6760 39 901 1383 1953 2343 2627 2825 3087 6761 40 912 1384 1961 2345 2629 2826 3091 6783 41 915 1385 1967 2346 2631 2830 3093 6788 48 929 1389 1968 2347 2632 2833 3094 6876 49 933 1390 1970 2353 2633 2835 3096 6883 62 958 1394 1976 2359 2634 2836 3099 6925 97 960 1397 1978 2360 2636 2838 3103 6998 113 961 1399 1991 2363 2638 2840 3107 7036 117 963 1400 1992 2364 2639 2850 3108 7067 121 964 1401 2048 2365 2644 2865 3111 7103 123 966 1402 2060 2370 2647 2871 3112 7121 139 967 1404 2086 2371 2648 2874 3116 7142 140 978 1405 2091 2382 2649 2877 3120 7154 141 987 1406 2092 2395 2653 2878 3121 7242 142 1006 1410 2093 2400 2654 2880 3123 7262 144 1007 1415 2094 2403 2656 2881 3124 7267 147 1008 1419 2104 2405 2657 2886 3125 7293 156 1009 1422 2112 2449 2660 2887 3126 7335 190 1011 1423 2114 2503 2666 2888 3130 7397 191 1012 1424 2115 2504 2667 2890 3136 7443 192 1015 1441 2117 2505 2675 2893 4501 7476 195 1016 1540 2132 2506 2676 2895 4502 7496 199 1017 1543 2137 2507 2678 2901 4503 7509 212 1018 1550 2144 2508 2681 2903 4504 7555 213 1019 1553 2145 2510 2700 2904 4505 7587 219 1020 1616 2148 2511 2701 2905 4506 7588 228 1021 1618 2149 2512 2711 2909 4507 7660 232 1022 1619 2158 2513 2712 2913 4508 7667 239 1023 1666 2161 2514 2713 2914 4509 252 1025 1668 2165 2515 2714 2916 4510 258 1029 1672 2172 2518 2715 2920 4511 268 1033 1677 2174 2519 2716 2922 4512 300 1034 1679 2192 2521 2718 2927 4513 303 1037 1682 2196 2525 2721 2928 4514 313 1038 1686 2225 2526 2723 2929 4515 316 1039 1690 2226 2527 2726 2930 4516 317 1043 1691 2227 2528 2731 2932 4517 318 1044 1695 2231 2529 2734 2933 4518 320 1046 1698 2235 2530 2737 2937 4519 332 1047 1721 2236 2531 2741 2943 4520 341 1049 1754 2249 2534 2744 2948 4521 346 1052 1759 2280 2535 2745 2950 4522 352 1056 1769 2299 2536 2748 2953 4523 363 1059 1770 2300 2539 2760 2957 4524 384 1060 1772 2301 2542 2772 2966 4525 386 1061 1773 2302 2544 2780 2967 4526 392 1076 1856 2303 2547 2781 2972 4527 396 1083 1857 2304 2548 2782 2976 4528 480 1093 1860 2305 2550 2783 2982 4529 550 1115 1861 2308 2551 2784 2983 4530 590 1137 1863 2309 2553 2786 2991 4531 591 1168 1864 2311 2556 2787 2995 4532 647 1171 1865 2312 2559 2788 3007 4533 715 1197 1867 2313 2561 2789 3014 4534 800 1198 1868 2314 2562 2790 3015 4535 801 1202 1870 2315 2566 2791 3018 4536 804 1203 1871 2316 2568 2792 3026 4537 805 1210 1874 2317 2573 2794 3035 4538 806 1216 1875 2319 2578 2795 3039 4539 818 1219 1876 2320 2583 2797 3042 4540 819 1225 1877 2322 2585 2798 3044 4541 871 1235 1881 2323 2592 2800 3045 6030 872 1242 1883 2324 2599 2801 3052 6073 873 1262 1889 2325 2610 2802 3053 6091 874 1371 1899 2326 2611 2804 3057 6181 876 1372 1937 2327 2612 2808 3059 6312 878 1373 1938 2328 2614 2810 3063 6402 880 1374 1939 2329 2615 2813 3065 6434 882 1375 1940 2331 2618 2815 3067 6505

TABLE D10 Gene modifying polypeptide candidates having a Z-score of at least 1 or greater in at least one condition. SEQ ID NOs: 1 596 1217 1846 2365 2884 6111 6610 7109 7608 2 597 1218 1847 2366 2885 6112 6611 7110 7609 3 598 1219 1848 2367 2886 6113 6612 7111 7610 4 599 1220 1849 2368 2887 6114 6613 7112 7611 5 600 1221 1850 2369 2888 6115 6614 7113 7612 6 601 1222 1851 2370 2889 6116 6615 7114 7613 7 602 1223 1852 2371 2890 6117 6616 7115 7614 9 603 1224 1853 2372 2891 6118 6617 7116 7615 10 604 1225 1854 2373 2892 6119 6618 7117 7616 12 605 1226 1855 2374 2893 6120 6619 7118 7617 13 606 1227 1856 2375 2894 6121 6620 7119 7618 14 607 1228 1857 2376 2895 6122 6621 7120 7619 17 610 1229 1858 2377 2896 6123 6622 7121 7620 18 611 1230 1859 2378 2897 6124 6623 7122 7621 19 613 1231 1860 2379 2898 6125 6624 7123 7622 22 614 1232 1861 2380 2899 6126 6625 7124 7623 24 616 1233 1862 2381 2900 6127 6626 7125 7624 28 617 1234 1863 2382 2901 6128 6627 7126 7625 33 618 1235 1864 2383 2902 6129 6628 7127 7626 34 624 1236 1865 2384 2903 6130 6629 7128 7627 35 625 1237 1866 2385 2904 6131 6630 7129 7628 36 626 1238 1867 2386 2905 6132 6631 7130 7629 37 628 1239 1868 2387 2906 6133 6632 7131 7630 38 631 1240 1869 2388 2907 6134 6633 7132 7631 39 632 1241 1870 2389 2908 6135 6634 7133 7632 40 633 1242 1871 2390 2909 6136 6635 7134 7633 41 634 1243 1872 2391 2910 6137 6636 7135 7634 42 636 1244 1873 2392 2911 6138 6637 7136 7635 43 638 1245 1874 2393 2912 6139 6638 7137 7636 44 640 1246 1875 2394 2913 6140 6639 7138 7637 45 645 1247 1876 2395 2914 6141 6640 7139 7638 46 647 1248 1877 2396 2915 6142 6641 7140 7639 47 648 1249 1878 2397 2916 6143 6642 7141 7640 48 649 1250 1879 2398 2917 6144 6643 7142 7641 49 650 1251 1880 2399 2918 6145 6644 7143 7642 50 651 1252 1881 2400 2919 6146 6645 7144 7643 51 652 1253 1882 2401 2920 6147 6646 7145 7644 52 653 1254 1883 2402 2921 6148 6647 7146 7645 53 654 1255 1884 2403 2922 6149 6648 7147 7646 54 655 1256 1885 2404 2923 6150 6649 7148 7647 55 656 1257 1886 2405 2924 6151 6650 7149 7648 56 657 1258 1887 2406 2925 6152 6651 7150 7649 57 659 1259 1888 2407 2926 6153 6652 7151 7650 58 660 1260 1889 2408 2927 6154 6653 7152 7651 59 661 1261 1890 2409 2928 6155 6654 7153 7652 60 662 1262 1891 2410 2929 6156 6655 7154 7653 61 663 1263 1892 2411 2930 6157 6656 7155 7654 62 664 1264 1893 2412 2931 6158 6657 7156 7655 63 666 1265 1894 2413 2932 6159 6658 7157 7656 64 667 1266 1895 2414 2933 6160 6659 7158 7657 65 668 1267 1896 2415 2934 6161 6660 7159 7658 66 669 1268 1897 2416 2935 6162 6661 7160 7659 67 670 1269 1898 2417 2936 6163 6662 7161 7660 68 673 1270 1899 2418 2937 6164 6663 7162 7661 69 674 1271 1900 2419 2938 6165 6664 7163 7662 70 675 1272 1901 2420 2939 6166 6665 7164 7663 71 676 1273 1902 2422 2940 6167 6666 7165 7664 72 677 1274 1903 2423 2941 6168 6667 7166 7665 73 678 1275 1904 2424 2942 6169 6668 7167 7666 74 679 1276 1905 2425 2943 6170 6669 7168 7667 75 680 1277 1906 2426 2944 6171 6670 7169 7668 76 681 1278 1907 2427 2945 6172 6671 7170 7669 77 684 1279 1908 2431 2946 6173 6672 7171 7670 78 687 1280 1909 2436 2947 6174 6673 7172 7671 79 689 1281 1910 2438 2948 6175 6674 7173 7672 80 690 1282 1911 2440 2949 6176 6675 7174 7673 81 692 1288 1912 2441 2950 6177 6676 7175 7674 82 694 1290 1913 2442 2951 6178 6677 7176 7675 83 700 1295 1914 2443 2952 6179 6678 7177 7676 84 702 1296 1915 2444 2953 6180 6679 7178 7677 85 704 1298 1916 2445 2954 6181 6680 7179 7678 86 706 1299 1917 2446 2955 6182 6681 7180 7679 87 707 1301 1918 2447 2957 6183 6682 7181 7680 88 711 1302 1919 2448 2958 6184 6683 7182 7681 89 715 1304 1920 2449 2959 6185 6684 7183 7682 90 716 1305 1921 2450 2960 6186 6685 7184 7683 91 717 1308 1922 2451 2962 6187 6686 7185 7684 92 719 1311 1923 2452 2965 6188 6687 7186 7685 93 720 1312 1924 2453 2966 6189 6688 7187 7686 94 722 1314 1925 2454 2967 6190 6689 7188 7687 95 724 1315 1926 2455 2968 6191 6690 7189 7688 96 726 1319 1927 2456 2969 6192 6691 7190 7689 97 727 1320 1928 2457 2970 6193 6692 7191 7690 98 728 1322 1929 2458 2971 6194 6693 7192 7691 99 729 1324 1931 2459 2972 6195 6694 7193 7692 100 731 1326 1932 2460 2973 6196 6695 7194 7693 101 738 1327 1933 2461 2974 6197 6696 7195 7694 102 739 1328 1934 2462 2975 6198 6697 7196 7695 103 740 1329 1935 2463 2976 6199 6698 7197 7696 104 745 1330 1936 2464 2977 6200 6699 7198 7697 105 746 1338 1937 2465 2978 6201 6700 7199 7698 106 747 1340 1938 2466 2979 6202 6701 7200 7699 107 755 1342 1939 2467 2980 6203 6702 7201 7700 108 756 1343 1940 2468 2981 6204 6703 7202 7701 110 759 1346 1941 2469 2982 6205 6704 7203 7702 111 765 1347 1942 2470 2983 6206 6705 7204 7703 112 766 1348 1943 2471 2984 6207 6706 7205 7704 113 767 1349 1944 2472 2985 6208 6707 7206 7705 114 768 1350 1945 2473 2986 6209 6708 7207 7706 115 769 1351 1946 2474 2987 6210 6709 7208 7707 116 770 1353 1947 2476 2988 6211 6710 7209 7708 117 771 1354 1948 2477 2989 6212 6711 7210 7709 118 772 1357 1949 2478 2990 6213 6712 7211 7710 119 773 1359 1950 2479 2991 6214 6713 7212 7711 120 774 1362 1951 2480 2992 6215 6714 7213 7712 121 775 1365 1952 2481 2993 6216 6715 7214 7713 122 776 1366 1953 2482 2994 6217 6716 7215 7714 123 777 1369 1954 2483 2995 6218 6717 7216 7715 124 780 1370 1955 2484 2996 6219 6718 7217 7716 125 781 1371 1956 2485 2997 6220 6719 7218 7717 126 782 1372 1957 2486 2998 6221 6720 7219 7718 127 783 1373 1958 2488 2999 6222 6721 7220 7719 128 784 1374 1959 2489 3001 6223 6722 7221 7720 129 785 1375 1960 2490 3002 6224 6723 7222 7721 130 789 1376 1961 2491 3003 6225 6724 7223 7722 131 790 1377 1962 2492 3004 6226 6725 7224 7723 132 794 1378 1963 2496 3005 6227 6726 7225 7724 133 797 1379 1964 2497 3006 6228 6727 7226 7725 134 798 1380 1965 2498 3007 6229 6728 7227 7726 135 799 1381 1966 2501 3008 6230 6729 7228 7727 136 800 1382 1967 2502 3009 6231 6730 7229 7728 137 801 1383 1968 2503 3010 6232 6731 7230 7729 138 802 1384 1969 2504 3011 6233 6732 7231 7730 139 803 1385 1970 2505 3012 6234 6733 7232 7731 140 804 1386 1971 2506 3013 6235 6734 7233 7732 141 805 1387 1972 2507 3014 6236 6735 7234 7733 142 806 1388 1973 2508 3015 6237 6736 7235 7734 143 807 1389 1974 2509 3016 6238 6737 7236 7735 144 808 1390 1975 2510 3017 6239 6738 7237 7736 145 809 1391 1976 2511 3018 6240 6739 7238 7737 146 810 1392 1977 2512 3019 6241 6740 7239 7738 147 811 1393 1978 2513 3020 6242 6741 7240 7739 148 812 1394 1979 2514 3021 6243 6742 7241 7740 149 813 1395 1980 2515 3022 6244 6743 7242 7741 150 814 1396 1981 2516 3023 6245 6744 7243 7742 151 815 1397 1982 2517 3024 6246 6745 7244 7743 152 816 1398 1983 2518 3025 6247 6746 7245 153 817 1399 1984 2519 3026 6248 6747 7246 154 818 1400 1985 2520 3027 6249 6748 7247 155 819 1401 1986 2521 3028 6250 6749 7248 156 820 1402 1987 2522 3029 6251 6750 7249 157 821 1403 1988 2523 3030 6252 6751 7250 158 822 1404 1989 2524 3031 6253 6752 7251 159 823 1405 1990 2525 3032 6254 6753 7252 160 824 1406 1991 2526 3033 6255 6754 7253 161 825 1407 1992 2527 3034 6256 6755 7254 162 826 1408 1993 2528 3035 6257 6756 7255 163 827 1409 1994 2529 3036 6258 6757 7256 164 828 1410 1995 2530 3037 6259 6758 7257 165 829 1411 1996 2531 3038 6260 6759 7258 166 830 1412 1997 2532 3039 6261 6760 7259 167 831 1413 1998 2533 3040 6262 6761 7260 168 832 1414 1999 2534 3041 6263 6762 7261 169 833 1415 2000 2535 3042 6264 6763 7262 170 834 1416 2001 2536 3043 6265 6764 7263 171 835 1417 2002 2537 3044 6266 6765 7264 172 836 1418 2003 2538 3045 6267 6766 7265 173 837 1419 2004 2539 3046 6268 6767 7266 174 839 1420 2005 2540 3047 6269 6768 7267 175 840 1421 2006 2541 3048 6270 6769 7268 176 841 1422 2007 2542 3049 6271 6770 7269 177 842 1423 2008 2543 3050 6272 6771 7270 178 843 1424 2009 2544 3051 6273 6772 7271 179 844 1425 2010 2545 3052 6274 6773 7272 180 845 1426 2011 2546 3053 6275 6774 7273 181 846 1427 2012 2547 3054 6276 6775 7274 182 847 1428 2013 2548 3055 6277 6776 7275 183 848 1429 2014 2549 3056 6278 6777 7276 184 849 1430 2015 2550 3057 6279 6778 7277 185 850 1431 2016 2551 3058 6280 6779 7278 186 851 1432 2017 2552 3059 6281 6780 7279 187 852 1433 2018 2553 3060 6282 6781 7280 188 853 1434 2019 2554 3061 6283 6782 7281 190 854 1435 2020 2555 3062 6284 6783 7282 191 855 1436 2021 2556 3063 6285 6784 7283 192 856 1437 2022 2557 3064 6286 6785 7284 193 857 1439 2023 2558 3065 6287 6786 7285 194 860 1440 2024 2559 3066 6288 6787 7286 195 861 1441 2025 2560 3067 6289 6788 7287 196 862 1442 2026 2561 3068 6290 6789 7288 197 863 1443 2027 2562 3069 6291 6790 7289 198 866 1444 2028 2563 3070 6292 6791 7290 199 867 1445 2029 2564 3071 6293 6792 7291 200 868 1446 2030 2565 3072 6294 6793 7292 201 869 1447 2031 2566 3073 6295 6794 7293 202 870 1448 2032 2567 3074 6296 6795 7294 203 871 1449 2033 2568 3075 6297 6796 7295 204 872 1450 2034 2569 3076 6298 6797 7296 205 873 1451 2035 2570 3077 6299 6798 7297 206 874 1452 2036 2571 3078 6300 6799 7298 207 875 1454 2037 2572 3079 6301 6800 7299 208 876 1455 2038 2573 3080 6302 6801 7300 209 877 1456 2039 2574 3081 6303 6802 7301 210 878 1460 2040 2575 3082 6304 6803 7302 211 879 1462 2041 2576 3083 6305 6804 7303 212 880 1465 2042 2577 3084 6306 6805 7304 213 881 1469 2043 2578 3085 6307 6806 7305 214 882 1471 2044 2579 3086 6308 6807 7306 215 883 1473 2045 2580 3087 6309 6808 7307 216 884 1475 2046 2581 3088 6310 6809 7308 217 885 1488 2047 2582 3089 6311 6810 7309 218 886 1489 2048 2583 3090 6312 6811 7310 219 887 1491 2049 2584 3091 6313 6812 7311 220 888 1492 2050 2585 3092 6314 6813 7312 221 889 1493 2051 2586 3093 6315 6814 7313 222 890 1497 2052 2587 3094 6316 6815 7314 223 891 1499 2053 2588 3095 6317 6816 7315 224 892 1504 2054 2589 3096 6318 6817 7316 225 893 1505 2055 2590 3097 6319 6818 7317 226 894 1506 2056 2591 3098 6320 6819 7318 227 895 1507 2057 2592 3099 6321 6820 7319 228 896 1508 2058 2593 3100 6322 6821 7320 229 897 1510 2059 2594 3101 6323 6822 7321 230 898 1513 2060 2595 3102 6324 6823 7322 231 899 1515 2061 2596 3103 6325 6824 7323 232 900 1519 2062 2597 3104 6326 6825 7324 233 901 1521 2063 2598 3105 6327 6826 7325 234 902 1523 2064 2599 3106 6328 6827 7326 235 903 1524 2066 2600 3107 6329 6828 7327 236 904 1527 2069 2601 3108 6330 6829 7328 237 905 1529 2070 2602 3109 6331 6830 7329 238 906 1531 2071 2603 3110 6332 6831 7330 239 907 1539 2072 2604 3111 6333 6832 7331 240 908 1540 2074 2605 3112 6334 6833 7332 241 909 1541 2075 2606 3113 6335 6834 7333 242 910 1542 2076 2607 3114 6336 6835 7334 243 911 1543 2079 2608 3115 6337 6836 7335 244 912 1544 2080 2610 3116 6338 6837 7336 245 913 1545 2081 2611 3117 6339 6838 7337 246 914 1546 2082 2612 3118 6340 6839 7338 247 915 1547 2084 2613 3119 6341 6840 7339 248 916 1548 2085 2614 3120 6342 6841 7340 249 917 1549 2086 2615 3121 6343 6842 7341 250 918 1550 2087 2616 3122 6344 6843 7342 251 919 1551 2088 2617 3123 6345 6844 7343 252 920 1552 2089 2618 3124 6346 6845 7344 253 921 1553 2090 2619 3125 6347 6846 7345 254 922 1554 2091 2620 3126 6348 6847 7346 255 923 1555 2092 2621 3127 6349 6848 7347 256 924 1556 2093 2622 3128 6350 6849 7348 257 925 1557 2094 2623 3129 6351 6850 7349 258 926 1558 2095 2624 3130 6352 6851 7350 259 927 1559 2096 2625 3131 6353 6852 7351 260 928 1560 2097 2626 3132 6354 6853 7352 261 929 1561 2098 2627 3133 6355 6854 7353 262 930 1563 2099 2628 3134 6356 6855 7354 263 931 1564 2100 2629 3135 6357 6856 7355 264 932 1565 2101 2630 3136 6358 6857 7356 265 933 1566 2102 2631 3138 6359 6858 7357 266 934 1567 2103 2632 3139 6360 6859 7358 267 935 1568 2104 2633 3141 6361 6860 7359 268 936 1570 2105 2634 3142 6362 6861 7360 269 937 1571 2106 2635 3144 6363 6862 7361 270 938 1572 2107 2636 3146 6364 6863 7362 271 939 1573 2108 2637 3147 6365 6864 7363 272 940 1574 2109 2638 3149 6366 6865 7364 273 941 1575 2110 2639 3152 6367 6866 7365 274 942 1576 2111 2640 3153 6368 6867 7366 275 943 1577 2112 2641 3154 6369 6868 7367 276 944 1578 2113 2642 3155 6370 6869 7368 277 945 1579 2114 2643 3157 6371 6870 7369 278 946 1580 2115 2644 3162 6372 6871 7370 279 947 1581 2116 2645 3163 6373 6872 7371 280 948 1582 2117 2646 3166 6374 6873 7372 281 950 1583 2118 2647 3167 6375 6874 7373 283 951 1584 2119 2648 3169 6376 6875 7374 284 952 1585 2120 2649 3171 6377 6876 7375 285 957 1587 2121 2650 3172 6378 6877 7376 286 958 1588 2122 2651 3173 6379 6878 7377 287 959 1590 2123 2652 3175 6380 6879 7378 288 960 1592 2124 2653 3176 6381 6880 7379 290 961 1593 2125 2654 3177 6382 6881 7380 292 962 1594 2126 2655 3180 6383 6882 7381 293 963 1595 2127 2656 3181 6384 6883 7382 294 964 1596 2128 2657 3183 6385 6884 7383 295 965 1597 2129 2658 3184 6386 6885 7384 296 966 1598 2130 2659 3188 6387 6886 7385 297 967 1599 2131 2660 3190 6388 6887 7386 298 968 1600 2132 2661 3194 6389 6888 7387 299 969 1604 2133 2662 3196 6390 6889 7388 300 970 1605 2134 2663 3198 6391 6890 7389 301 971 1606 2135 2664 3199 6392 6891 7390 302 972 1607 2136 2665 3201 6393 6892 7391 303 973 1608 2137 2666 3202 6394 6893 7392 304 974 1610 2138 2667 3203 6395 6894 7393 305 975 1611 2139 2668 3204 6396 6895 7394 306 976 1612 2140 2669 3205 6397 6896 7395 307 977 1616 2141 2670 3206 6398 6897 7396 308 978 1617 2142 2671 3207 6399 6898 7397 309 979 1618 2143 2672 3208 6400 6899 7398 310 980 1619 2144 2673 3209 6401 6900 7399 311 981 1620 2145 2674 3211 6402 6901 7400 312 982 1621 2146 2675 3213 6403 6902 7401 313 983 1622 2147 2676 3214 6404 6903 7402 314 984 1623 2148 2677 3218 6405 6904 7403 315 985 1624 2149 2678 3219 6406 6905 7404 316 986 1625 2150 2679 3220 6407 6906 7405 317 987 1626 2151 2680 3223 6408 6907 7406 318 988 1627 2152 2681 3225 6409 6908 7407 319 989 1628 2153 2682 3228 6410 6909 7408 320 990 1629 2154 2683 3231 6411 6910 7409 321 991 1630 2155 2684 3233 6412 6911 7410 322 992 1631 2156 2685 3234 6413 6912 7411 323 993 1632 2157 2686 3235 6414 6913 7412 324 994 1633 2158 2687 3240 6415 6914 7413 325 995 1634 2159 2688 3247 6416 6915 7414 326 996 1635 2160 2689 3248 6417 6916 7415 327 997 1636 2161 2690 3251 6418 6917 7416 328 998 1637 2162 2691 3252 6419 6918 7417 329 999 1638 2163 2692 3253 6420 6919 7418 330 1000 1639 2164 2693 3254 6421 6920 7419 331 1001 1640 2165 2694 3256 6422 6921 7420 332 1002 1641 2166 2695 3259 6423 6922 7421 333 1003 1642 2167 2696 3260 6424 6923 7422 334 1004 1644 2168 2697 3261 6425 6924 7423 335 1005 1645 2169 2698 3262 6426 6925 7424 336 1006 1646 2170 2699 3263 6427 6926 7425 337 1007 1647 2171 2700 3264 6428 6927 7426 338 1008 1648 2172 2701 3265 6429 6928 7427 339 1009 1649 2173 2702 3266 6430 6929 7428 340 1010 1651 2174 2703 3268 6431 6930 7429 341 1011 1652 2175 2704 3269 6432 6931 7430 342 1012 1653 2176 2706 3270 6433 6932 7431 343 1013 1654 2177 2708 3272 6434 6933 7432 344 1014 1655 2178 2709 3276 6435 6934 7433 345 1015 1656 2179 2710 3277 6436 6935 7434 346 1016 1657 2180 2711 3279 6437 6936 7435 347 1017 1658 2181 2712 3282 6438 6937 7436 348 1018 1659 2182 2713 3283 6439 6938 7437 349 1019 1660 2183 2714 3286 6440 6939 7438 350 1020 1661 2184 2715 3294 6441 6940 7439 351 1021 1662 2185 2716 3296 6442 6941 7440 352 1022 1663 2186 2717 3298 6443 6942 7441 353 1023 1664 2187 2718 3299 6444 6943 7442 354 1024 1665 2188 2719 3300 6445 6944 7443 355 1025 1666 2189 2720 3302 6446 6945 7444 356 1026 1667 2190 2721 3303 6447 6946 7445 357 1027 1668 2191 2722 3305 6448 6947 7446 358 1028 1669 2192 2723 3306 6449 6948 7447 359 1029 1670 2193 2724 3310 6450 6949 7448 360 1030 1671 2194 2725 3313 6451 6950 7449 361 1031 1672 2195 2726 3315 6452 6951 7450 362 1032 1673 2196 2727 3316 6453 6952 7451 363 1033 1674 2197 2728 3317 6454 6953 7452 364 1034 1675 2198 2729 3318 6455 6954 7453 365 1035 1676 2199 2730 3323 6456 6955 7454 366 1036 1677 2200 2731 3326 6457 6956 7455 367 1037 1678 2201 2732 3329 6458 6957 7456 368 1038 1679 2202 2733 4501 6459 6958 7457 369 1039 1680 2203 2734 4502 6460 6959 7458 370 1040 1681 2204 2735 4503 6461 6960 7459 371 1041 1682 2205 2736 4504 6462 6961 7460 372 1042 1683 2206 2737 4505 6463 6962 7461 373 1043 1684 2207 2738 4506 6464 6963 7462 374 1044 1685 2208 2739 4507 6465 6964 7463 375 1045 1686 2209 2740 4508 6466 6965 7464 376 1046 1687 2210 2741 4509 6467 6966 7465 377 1047 1688 2211 2742 4510 6468 6967 7466 378 1048 1689 2212 2743 4511 6469 6968 7467 379 1049 1690 2213 2744 4512 6470 6969 7468 380 1050 1691 2214 2745 4513 6471 6970 7469 381 1051 1692 2215 2746 4514 6472 6971 7470 382 1052 1693 2218 2747 4515 6473 6972 7471 383 1053 1694 2219 2748 4516 6474 6973 7472 384 1054 1695 2220 2749 4517 6475 6974 7473 385 1055 1696 2222 2750 4518 6476 6975 7474 386 1056 1697 2223 2751 4519 6477 6976 7475 387 1057 1698 2224 2752 4520 6478 6977 7476 388 1058 1699 2225 2753 4521 6479 6978 7477 389 1059 1700 2226 2754 4522 6480 6979 7478 390 1060 1701 2227 2755 4523 6481 6980 7479 391 1061 1702 2228 2756 4524 6482 6981 7480 392 1062 1703 2229 2757 4525 6483 6982 7481 393 1063 1704 2230 2758 4526 6484 6983 7482 394 1064 1705 2231 2759 4527 6485 6984 7483 395 1065 1706 2232 2760 4528 6486 6985 7484 396 1066 1707 2233 2761 4529 6487 6986 7485 397 1067 1708 2234 2762 4530 6488 6987 7486 398 1068 1709 2235 2763 4531 6489 6988 7487 399 1069 1710 2236 2764 4532 6490 6989 7488 400 1070 1711 2237 2765 4533 6491 6990 7489 401 1071 1712 2238 2766 4534 6492 6991 7490 402 1072 1713 2239 2767 4535 6493 6992 7491 403 1073 1714 2240 2768 4536 6494 6993 7492 404 1074 1715 2241 2769 4537 6495 6994 7493 405 1075 1716 2242 2770 4538 6496 6995 7494 406 1076 1717 2243 2771 4539 6497 6996 7495 407 1077 1718 2244 2772 4540 6498 6997 7496 408 1078 1719 2245 2773 4541 6499 6998 7497 409 1079 1720 2246 2774 6001 6500 6999 7498 410 1080 1721 2247 2775 6002 6501 7000 7499 413 1081 1722 2248 2776 6003 6502 7001 7500 415 1082 1723 2249 2777 6004 6503 7002 7501 416 1083 1724 2250 2778 6005 6504 7003 7502 419 1084 1725 2251 2779 6006 6505 7004 7503 420 1085 1726 2252 2780 6007 6506 7005 7504 421 1086 1727 2253 2781 6008 6507 7006 7505 423 1087 1728 2254 2782 6009 6508 7007 7506 424 1088 1729 2255 2783 6010 6509 7008 7507 426 1089 1730 2256 2784 6011 6510 7009 7508 427 1090 1731 2257 2785 6012 6511 7010 7509 428 1091 1733 2259 2786 6013 6512 7011 7510 429 1092 1734 2260 2787 6014 6513 7012 7511 432 1093 1735 2261 2788 6015 6514 7013 7512 433 1094 1736 2262 2789 6016 6515 7014 7513 437 1095 1737 2263 2790 6017 6516 7015 7514 438 1096 1738 2264 2791 6018 6517 7016 7515 441 1097 1739 2265 2792 6019 6518 7017 7516 443 1103 1740 2266 2793 6020 6519 7018 7517 446 1110 1741 2268 2794 6021 6520 7019 7518 449 1115 1742 2270 2795 6022 6521 7020 7519 450 1116 1743 2271 2796 6023 6522 7021 7520 452 1117 1744 2272 2797 6024 6523 7022 7521 460 1118 1745 2273 2798 6025 6524 7023 7522 461 1119 1746 2274 2799 6026 6525 7024 7523 462 1120 1747 2275 2800 6027 6526 7025 7524 464 1121 1748 2276 2801 6028 6527 7026 7525 465 1122 1750 2277 2802 6029 6528 7027 7526 469 1123 1751 2278 2803 6030 6529 7028 7527 470 1124 1752 2279 2804 6031 6530 7029 7528 472 1126 1753 2280 2805 6032 6531 7030 7529 474 1127 1754 2281 2806 6033 6532 7031 7530 475 1129 1755 2282 2807 6034 6533 7032 7531 476 1131 1756 2283 2808 6035 6534 7033 7532 480 1134 1757 2286 2809 6036 6535 7034 7533 481 1136 1758 2287 2810 6037 6536 7035 7534 483 1137 1759 2288 2811 6038 6537 7036 7535 484 1138 1760 2289 2812 6039 6538 7037 7536 486 1139 1761 2291 2813 6040 6539 7038 7537 488 1140 1762 2292 2814 6041 6540 7039 7538 489 1141 1764 2293 2815 6042 6541 7040 7539 495 1142 1765 2294 2816 6043 6542 7041 7540 498 1143 1766 2295 2817 6044 6543 7042 7541 499 1144 1767 2299 2818 6045 6544 7043 7542 502 1145 1768 2300 2819 6046 6545 7044 7543 503 1146 1769 2301 2820 6047 6546 7045 7544 504 1147 1770 2302 2821 6048 6547 7046 7545 510 1148 1771 2303 2822 6049 6548 7047 7546 517 1149 1772 2304 2823 6050 6549 7048 7547 519 1150 1773 2305 2824 6051 6550 7049 7548 522 1151 1774 2306 2825 6052 6551 7050 7549 523 1152 1775 2307 2826 6053 6552 7051 7550 524 1153 1776 2308 2827 6054 6553 7052 7551 527 1154 1777 2309 2828 6055 6554 7053 7552 528 1155 1778 2310 2829 6056 6555 7054 7553 532 1156 1779 2311 2830 6057 6556 7055 7554 534 1157 1780 2312 2831 6058 6557 7056 7555 535 1158 1781 2313 2832 6059 6558 7057 7556 536 1159 1782 2314 2833 6060 6559 7058 7557 537 1160 1783 2315 2834 6061 6560 7059 7558 538 1161 1784 2316 2835 6062 6561 7060 7559 539 1162 1785 2317 2836 6063 6562 7061 7560 540 1163 1786 2318 2837 6064 6563 7062 7561 541 1164 1787 2319 2838 6065 6564 7063 7562 542 1165 1788 2320 2839 6066 6565 7064 7563 543 1166 1789 2321 2840 6067 6566 7065 7564 544 1167 1790 2322 2841 6068 6567 7066 7565 545 1168 1791 2323 2842 6069 6568 7067 7566 546 1169 1792 2324 2843 6070 6569 7068 7567 547 1170 1793 2325 2844 6071 6570 7069 7568 548 1171 1794 2326 2845 6072 6571 7070 7569 549 1172 1795 2327 2846 6073 6572 7071 7570 550 1173 1796 2328 2847 6074 6573 7072 7571 553 1174 1797 2329 2848 6075 6574 7073 7572 554 1176 1799 2330 2849 6076 6575 7074 7573 555 1177 1800 2331 2850 6077 6576 7075 7574 556 1178 1801 2332 2851 6078 6577 7076 7575 557 1179 1802 2333 2852 6079 6578 7077 7576 558 1181 1803 2334 2853 6080 6579 7078 7577 559 1182 1804 2335 2854 6081 6580 7079 7578 560 1184 1805 2336 2855 6082 6581 7080 7579 561 1185 1806 2337 2856 6083 6582 7081 7580 562 1186 1808 2338 2857 6084 6583 7082 7581 563 1187 1809 2339 2858 6085 6584 7083 7582 564 1188 1810 2340 2859 6086 6585 7084 7583 565 1190 1811 2341 2860 6087 6586 7085 7584 566 1193 1812 2342 2861 6088 6587 7086 7585 567 1195 1813 2343 2862 6089 6588 7087 7586 568 1196 1815 2344 2863 6090 6589 7088 7587 569 1197 1816 2345 2864 6091 6590 7089 7588 570 1198 1817 2346 2865 6092 6591 7090 7589 571 1199 1818 2347 2866 6093 6592 7091 7590 572 1200 1819 2348 2867 6094 6593 7092 7591 575 1201 1823 2349 2868 6095 6594 7093 7592 580 1202 1824 2350 2869 6096 6595 7094 7593 581 1203 1825 2351 2870 6097 6596 7095 7594 583 1204 1827 2352 2871 6098 6597 7096 7595 584 1205 1828 2353 2872 6099 6598 7097 7596 585 1206 1829 2354 2873 6100 6599 7098 7597 586 1207 1831 2355 2874 6101 6600 7099 7598 587 1208 1832 2356 2875 6102 6601 7100 7599 588 1209 1834 2357 2876 6103 6602 7101 7600 589 1210 1835 2358 2877 6104 6603 7102 7601 590 1211 1838 2359 2878 6105 6604 7103 7602 591 1212 1840 2360 2879 6106 6605 7104 7603 592 1213 1842 2361 2880 6107 6606 7105 7604 593 1214 1843 2362 2881 6108 6607 7106 7605 594 1215 1844 2363 2882 6109 6608 7107 7606 595 1216 1845 2364 2883 6110 6609 7108 7607

As the results in this example establish, gene modifying polypeptides combining linkers selected PG-8T, from those shown in Table 10 and RTs from 17 retroviral RT families out of the 35 RT families screened have gene editing activity when delivered as DNA to test cells.

Example 4: Evaluating the Effects of RT Domain Mutations on Editing Activity in Pooled Screen

The pooled screen data using the library from Example 3 was further analyzed to evaluate the effect of mutations, within and across RT families, on candidate gene modifying polypeptide editing activity. The RT families included RT domains comprising one or more substitutions at positions corresponding to 200, 603, 330, 524, 562, 583, 51, 67, 67, 197, 204, 302, 309, 313, 435, 454, 594, 671, 69, or 653 of murine leukemia virus reverse transcriptase relative to a wildtype sequence of the RT domain. Without wishing to be bound by theory, it is thought that substitutions at positions corresponding to one or more of these positions may improve stability (e.g., thermostability) and/or editing activity of the RT domain and/or a gene modifying polypeptide comprising the same. Specific combinations of mutations tested included those listed in Table 2.

FIGS. 8A-8F, 9A-9H, and 10A-10C show graphs of average Z score for candidate gene modifying polypeptides grouped by RT variant (X-axis) and RT family (each box).

FIGS. 8A-8F show that for several RT families (MLVAV, MLVBM, BAEVM, FLV, FOAMV, and GALV), gene modifying polypeptide candidates comprising RT variants without mutations have negative or near 0 average Z-scores, whereas those comprising RT variants with one or more mutations at the specified sites have positive average Z-scores which increase with the number of positions substituted. These results show that mutations at one or more of the positions suspected of stabilizing/increasing editing activity rescue RT domains of these families, resulting in active or more active candidate gene modifying polypeptides relative to gene candidates with an RT lacking substitutions.

FIGS. 9A-9H show that for several RT families (KORV, AVIRE, MLVCB, MLVFF, MLVMS, SFV3L, WMSV, and XMRV6), gene modifying polypeptide candidates comprising RT variants without mutations have positive average Z-scores and those comprising RT variants with one or more mutations at the specified sites have higher average Z-scores which increase with the number of positions substituted. These results show that for eight of the RT families tested, mutations at one or more of the positions suspected of stabilizing/increasing editing activity further improve the activity of already active RT domains in these families, resulting in more active candidate gene modifying polypeptides.

FIGS. 10A-10C show that for several RT families that show editing activity in Example 3 (PERV, SFV1, and FFV), gene modifying polypeptide candidates comprising RT variants without mutations have similar average Z-scores to those comprising RT variants with one or more mutations at the specified sites, or have lower average Z-scores that decrease with the number of positions substituted. These results show that the effect of mutations is not predictable as evidenced by the fact that, for some editing-active RT families, mutations at one or more of the positions suspected of stabilizing/increasing editing activity have no or little effect on editing activity, or decrease the editing activity of the gene modifying polypeptide.

These results demonstrate that RT domain mutations at one or more positions corresponding to 200, 603, 330, 524, 562, 583, 51, 67, 67, 197, 204, 302, 309, 313, 435, 454, 594, 671, 69, or 653 of murine leukemia virus reverse transcriptase can increase editing activity of gene modifying polypeptides derived from certain RT families and not others. In particular, editing activity of candidate gene modifying polypeptides containing RT domains of RT families MLVAV, MLVBM, BAEVM, FLV, FOAMV, GALV, KORV, AVIRE, MLVCB, MLVFF, MLVMS, SFV3L, WMSV, and XMRV6 was increased by substitutions at the listed positions, and that the more substitutions in the RT variant, the greater the increase in editing activity. The RT families identified as active in Example 3 where substitutions improved editing activity were nearly all derived from Gammaretroviruses, with one gammaretroviral RT family (PERV) showing no effect on editing activity from the substitutions. Both of the RT families identified as active in Example 3 where substitutions negatively correlated with editing activity were Spumavirus RTs.

Example 5: Evaluating the Effects of Different Linkers on Editing Activity in Pooled Screen

The pooled screen data using the library from Example 3 was further analyzed to evaluate the effect of different linkers, within and across RT families, on candidate gene modifying polypeptide editing activity.

FIG. 11 shows a graph of average Z score for candidate gene modifying polypeptides grouped by linker (Y-axis) for select linkers, with lines indicating the average and standard error of the mean from the highest performing linker. The results show that candidate gene modifying polypeptides containing a

(SEQ ID NO: 11,041) AEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKEAAAKA linker consistently show high editing activity. The results further suggest that some linkers, e.g., those listed in Table A2, show higher editing activity than some other linkers tested.

TABLE A2 Exemplary Linkers Amino Acid Sequence SEQ ID NO: AEAAAKEAAAKEAAAKEAAAKALEAEAAAK 11,041 EAAAKEAAAKEAAAKA EAAAKEAAAKEAAAKEAAAKEAAAKEAAAK 11,042 SGGSSGGSSGSETPGTSESATPESSGGSSG 11,043 GSS EAAAKEAAAKEAAAKEAAAKEAAAK 11,044 EAAAKEAAAKEAAAKEAAAK 11,045 GSSGSSGSSGSSGSSGSS 11,046 GGGGSGGGGSGGGGSGGGGSGGGGSGGGGS 11,047 SGSETPGTSESATPES 11,048 PAPAPAPAPAPAP 11,049 EAAAKGGGGSEAAAK 11,050

Example 6: Characterizing Editing Activity of Exemplary Gene Modifying Polypeptides Delivered in RNA Form to Several Model Systems

FIG. 12A-12D show graphs of editing activity of four exemplary gene modifying polypeptides delivered as RNA in different experimental model systems, each gene modifying polypeptide comprising the AEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKEAAAKA (SEQ ID NO: 11,041) linker. The amino acid sequences of the exemplary gene modifying polypeptides are given in the below table.

TABLE A3 Exemplary Gene Modifying Polypeptides Exemplary Gene Modifying Polypeptide Full AA Sequence 1 MPAAKRVKLDGGDKKYSIGLDIGTNSVGWA VITDEYKVPSKKFKVLGNTDRHSIKKNLIG ALLFDSGETAEATRLKRTARRRYTRRKNRI CYLQEIFSNEMAKVDDSFFHRLEESFLVEE DKKHERHPIFGNIVDEVAYHEKYPTIYHLR KKLVDSTDKADLRLIYLALAHMIKFRGHFL IEGDLNPDNSDVDKLFIQLVQTYNQLFEEN PINASGVDAKAILSARLSKSRRLENLIAQL PGEKKNGLFGNLIALSLGLTPNFKSNFDLA EDAKLQLSKDTYDDDLDNLLAQIGDQYADL FLAAKNLSDAILLSDILRVNTEITKAPLSA SMIKRYDEHHQDLTLLKALVRQQLPEKYKE IFFDQSKNGYAGYIDGGASQEEFYKFIKPI LEKMDGTEELLVKLNREDLLRKORTFDNGS IPHQIHLGELHAILRRQEDFYPFLKDNREK IEKILTFRIPYYVGPLARGNSRFAWMTRKS EETITPWNFEEVVDKGASAQSFIERMTNFD KNLPNEKVLPKHSLLYEYFTVYNELTKVKY VTEGMRKPAFLSGEQKKAIVDLLFKTNRKV TVKQLKEDYFKKIECFDSVEISGVEDRFNA SLGTYHDLLKIIKDKDFLDNEENEDILEDI VLTLTLFEDREMIEERLKTYAHLFDDKVMK QLKRRRYTGWGRLSRKLINGIRDKQSGKTI LDFLKSDGFANRNFMQLIHDDSLTFKEDIQ KAQVSGQGDSLHEHIANLAGSPAIKKGILQ TVKVVDELVKVMGRHKPENIVIEMARENQT TQKGQKNSRERMKRIEEGIKELGSQILKEH PVENTQLQNEKLYLYYLQNGRDMYVDQELD INRLSDYDVDHIVPQSFLKDDSIDNKVLTR SDKARGKSDNVPSEEVVKKMKNYWROLLNA KLITORKFDNLTKAERGGLSELDKAGFIKR QLVETRQITKHVAQILDSRMNTKYDENDKL IREVKVITLKSKLVSDFRKDFQFYKVREIN NYHHAHDAYLNAVVGTALIKKYPKLESEFV YGDYKVYDVRKMIAKSEQEIGKATAKYFFY SNIMNFFKTEITLANGEIRKRPLIETNGET GEIVWDKGRDFATVRKVLSMPQVNIVKKTE VQTGGFSKESILPKRNSDKLIARKKDWDPK KYGGFDSPTVAYSVLVVAKVEKGKSKKLKS VKELLGITIMERSSFEKNPIDFLEAKGYKE VKKDLIIKLPKYSLFELENGRKRMLASAGE LQKGNELALPSKYVNFLYLASHYEKLKGSP EDNEQKQLFVEQHKHYLDEIIEQISEFSKR VILADANLDKVLSAYNKHRDKPIREQAENI IHLFTLTNLGAPAAFKYFDTTIDRKRYTST KEVLDATLIHQSITGLYETRIDLSQLGGDG GAEAAAKEAAAKEAAAKEAAAKALEAEAAA KEAAAKEAAAKEAAAKAGGTAPLEEEYRLF LEAPIQNVTLLEQWKREIPKVWAEINPPGL ASTQAPIHVQLLSTALPVRVRQYPITLEAK RSLRETIRKFRAAGILRPVHSPWNTPLLPV RKSGTSEYRMVQDLREVNKRVETIHPTVPN PYTLLSLLPPDRIWYSVLDLKDAFFCIPLA PESQLIFAFEWADAEEGESGQLTWTRLPQG FKNSPTLFNEALNRDLQGFRLDHPSVSLLQ YVDDLLIAADTQAACLSATRDLLMTLAELG YRVSGKKAQLCQEEVTYLGFKIHKGSRSLS NSRTQAILQIPVPKTKRQVREFLGKIGYCR LFIPGFAELAQPLYAATRPGNDPLVWGEKE EEAFQSLKLALTQPPALALPSLDKPFQLFV EETSGAAKGVLTQALGPWKRPVAYLSKRLD PVAAGWPRCLRAIAAAALLTREASKLTFGQ DIEITSSHNLESLLRSPPDKWLTNARITQY QVLLLDPPRVRFKQTAALNPATLLPETDDT LPIHHCLDTLDSLTSTRPDLTDQPLAQAEA TLFTDGSSYIRDGKRYAGAAVVTLDSVIWA EPLPIGTSAQKAELIALTKALEWSKDKSVN IYTDSRYAFATLHVHGMIYRERGWLTAGGK AIKNAPEILALLTAVWLPKRVAVMHCKGHQ KDDAPTSTGNRRADEVAREVAIRPLSTQAT ISAGKRTADGSEFEKRTADGSEFESPKKKA KVE (SEQ ID NO: 11,091) 2 MPAAKRVKLDGGDKKYSIGLDIGTNSVGWA VITDEYKVPSKKFKVLGNTDRHSIKKNLIG ALLFDSGETAEATRLKRTARRRYTRRKNRI CYLQEIFSNEMAKVDDSFFHRLEESFLVEE DKKHERHPIFGNIVDEVAYHEKYPTIYHLR KKLVDSTDKADLRLIYLALAHMIKFRGHFL IEGDLNPDNSDVDKLFIQLVQTYNQLFEEN PINASGVDAKAILSARLSKSRRLENLIAQL PGEKKNGLFGNLIALSLGLTPNFKSNFDLA EDAKLQLSKDTYDDDLDNLLAQIGDQYADL FLAAKNLSDAILLSDILRVNTEITKAPLSA SMIKRYDEHHQDLTLLKALVRQQLPEKYKE IFFDQSKNGYAGYIDGGASQEEFYKFIKPI LEKMDGTEELLVKLNREDLLRKORTFDNGS IPHQIHLGELHAILRRQEDFYPFLKDNREK IEKILTFRIPYYVGPLARGNSRFAWMTRKS EETITPWNFEEVVDKGASAQSFIERMTNFD KNLPNEKVLPKHSLLYEYFTVYNELTKVKY VTEGMRKPAFLSGEQKKAIVDLLFKTNRKV TVKQLKEDYFKKIECFDSVEISGVEDRFNA SLGTYHDLLKIIKDKDFLDNEENEDILEDI VLTLTLFEDREMIEERLKTYAHLFDDKVMK QLKRRRYTGWGRLSRKLINGIRDKQSGKTI LDFLKSDGFANRNFMQLIHDDSLTFKEDIQ KAQVSGQGDSLHEHIANLAGSPAIKKGILQ TVKVVDELVKVMGRHKPENIVIEMARENQT TQKGQKNSRERMKRIEEGIKELGSQILKEH PVENTQLQNEKLYLYYLQNGRDMYVDQELD INRLSDYDVDHIVPQSFLKDDSIDNKVLTR SDKARGKSDNVPSEEVVKKMKNYWRQLLNA KLITQRKFDNLTKAERGGLSELDKAGFIKR QLVETRQITKHVAQILDSRMNTKYDENDKL IREVKVITLKSKLVSDFRKDFQFYKVREIN NYHHAHDAYLNAVVGTALIKKYPKLESEFV YGDYKVYDVRKMIAKSEQEIGKATAKYFFY SNIMNFFKTEITLANGEIRKRPLIETNGET GEIVWDKGRDFATVRKVLSMPQVNIVKKTE VQTGGFSKESILPKRNSDKLIARKKDWDPK KYGGFDSPTVAYSVLVVAKVEKGKSKKLKS VKELLGITIMERSSFEKNPIDFLEAKGYKE VKKDLIIKLPKYSLFELENGRKRMLASAGE LQKGNELALPSKYVNFLYLASHYEKLKGSP EDNEQKQLFVEQHKHYLDEIIEQISEFSKR VILADANLDKVLSAYNKHRDKPIREQAENI IHLFTLTNLGAPAAFKYFDTTIDRKRYTST KEVLDATLIHQSITGLYETRIDLSQLGGDG GAEAAAKEAAAKEAAAKEAAAKALEAEAAA KEAAAKEAAAKEAAAKAGGTLQLEEEYRLF EPESTQKQEMDIWLKNFPQAWAETGGMGTA HCQAPVLIQLKATATPISIRQYPMPHEAYQ GIKPHIRRMLDQGILKPCQSPWNTPLLPVK KPGTEDYRPVQDLREVNKRVEDIHPTVPNP YNLLSTLPPSHPWYTVLDLKDAFFCLRLHS ESQLLFAFEWRDPEIGLSGQLTWTRLPQGF KNSPTLFNEALHSDLADFRVRYPALVLLQY VDDLLLAAATRTECLEGTKALLETLGNKGY RASAKKAQICLQEVTYLGYSLKDGQRWLTK ARKEAILSIPVPKNSRQVREFLGKAGYCRL FIPGFAELAAPLYPLTRPGTLFQWGTEQQL AFEDIKKALLSSPALGLPDITKPFELFIDE NSGFAKGVLVQKLGPWKRPVAYLSKKLDTV ASGWPPCLRMVAAIAILVKDAGKLTLGQPL TILTSHPVEALVRQPPNKWLSNARMTHYQA MLLDAERVHFGPTVSLNPATLLPLPSGGNH HDCLQILAETHGTRPDLTDQPLPDADLTWY TDGSSFIRNGEREAGAAVTTESEVIWAAPL PPGTSAQRAELIALTQALKMAEGKKLTVYT DSRYAFATTHVHGEIYRRRGWLTSEGKEIK NKNEILALLEALFLPKRLSIIHCPGHQKGD SPQAKGNRLADDTAKKAATETHSSLTVLPA GKRTADGSEFEKRTADGSEFESPKKKAKVE (SEQ ID NO: 11,092) 3 MPAAKRVKLDGGDKKYSIGLDIGTNSVGWA VITDEYKVPSKKFKVLGNTDRHSIKKNLIG ALLFDSGETAEATRLKRTARRRYTRRKNRI CYLQEIFSNEMAKVDDSFFHRLEESFLVEE DKKHERHPIFGNIVDEVAYHEKYPTIYHLR KKLVDSTDKADLRLIYLALAHMIKFRGHFL IEGDLNPDNSDVDKLFIQLVQTYNQLFEEN PINASGVDAKAILSARLSKSRRLENLIAQL PGEKKNGLFGNLIALSLGLTPNFKSNFDLA EDAKLQLSKDTYDDDLDNLLAQIGDQYADL FLAAKNLSDAILLSDILRVNTEITKAPLSA SMIKRYDEHHQDLTLLKALVRQQLPEKYKE IFFDQSKNGYAGYIDGGASQEEFYKFIKPI LEKMDGTEELLVKLNREDLLRKORTFDNGS IPHQIHLGELHAILRRQEDFYPFLKDNREK IEKILTFRIPYYVGPLARGNSRFAWMTRKS EETITPWNFEEVVDKGASAQSFIERMTNFD KNLPNEKVLPKHSLLYEYFTVYNELTKVKY VTEGMRKPAFLSGEQKKAIVDLLFKTNRKV TVKQLKEDYFKKIECFDSVEISGVEDRFNA SLGTYHDLLKIIKDKDFLDNEENEDILEDI VLTLTLFEDREMIEERLKTYAHLFDDKVMK QLKRRRYTGWGRLSRKLINGIRDKQSGKTI LDFLKSDGFANRNFMQLIHDDSLTFKEDIQ KAQVSGQGDSLHEHIANLAGSPAIKKGILQ TVKVVDELVKVMGRHKPENIVIEMARENQT TQKGQKNSRERMKRIEEGIKELGSQILKEH PVENTQLQNEKLYLYYLQNGRDMYVDQELD INRLSDYDVDHIVPQSFLKDDSIDNKVLTR SDKARGKSDNVPSEEVVKKMKNYWRQLLNA KLITQRKFDNLTKAERGGLSELDKAGFIKR QLVETRQITKHVAQILDSRMNTKYDENDKL IREVKVITLKSKLVSDFRKDFQFYKVREIN NYHHAHDAYLNAVVGTALIKKYPKLESEFV YGDYKVYDVRKMIAKSEQEIGKATAKYFFY SNIMNFFKTEITLANGEIRKRPLIETNGET GEIVWDKGRDFATVRKVLSMPQVNIVKKTE VQTGGFSKESILPKRNSDKLIARKKDWDPK KYGGFDSPTVAYSVLVVAKVEKGKSKKLKS VKELLGITIMERSSFEKNPIDFLEAKGYKE VKKDLIIKLPKYSLFELENGRKRMLASAGE LQKGNELALPSKYVNFLYLASHYEKLKGSP EDNEQKQLFVEQHKHYLDEIIEQISEFSKR VILADANLDKVLSAYNKHRDKPIREQAENI IHLFTLTNLGAPAAFKYFDTTIDRKRYTST KEVLDATLIHQSITGLYETRIDLSQLGGDG GAEAAAKEAAAKEAAAKEAAAKALEAEAAA KEAAAKEAAAKEAAAKAGGTLNIEDEHRLH ETSKEPDVSLGSTWLSDFPQAWAETGGMGL AVRQAPLIIPLKATSTPVSIKQYPMSQEAR LGIKPHIQRLLDQGILVPCQSPWNTPLLPV KKPGTNDYRPVQDLREVNKRVEDIHPTVPN PYNLLSGLPPSHQWYTVLDLKDAFFCLRLH PTSQPLFAFEWRDPEMGISGQLTWTRLPQG FKNSPTLFNEALHRDLADFRIQHPDLILLQ YVDDLLLAATSELDCQQGTRALLQTLGNLG YRASAKKAQICQKQVKYLGYLLKEGQRWLT EARKETVMGQPTPKTPRQLREFLGKAGFCR LFIPGFAEMAAPLYPLTKPGTLFNWGPDQQ KAYQEIKQALLTAPALGLPDLTKPFELFVD EKQGYAKGVLTQKLGPWRRPVAYLSKKLDP VAAGWPPCLRMVAAIAVLTKDAGKLTMGQP LVILAPHAVEALVKQPPDRWLSNARMTHYQ ALLLDTDRVQFGPVVALNPATLLPLPEEGL QHNCLDILAEAHGTRPDLTDQPLPDADHTW YTDGSSLLQEGQRKAGAAVTTETEVIWAKA LPAGTSAQRAELIALTQALKMAEGKKLNVY TDSRYAFATAHIHGEIYRRRGWLTSEGKEI KNKDEILALLKALFLPKRLSIIHCPGHQKG HSAEARGNRMADQAARKAAITETPDTSTLL AGKRTADGSEFEKRTADGSEFESPKKKAKV E (SEQ ID NO: 11,093) 4 MPAAKRVKLDGGDKKYSIGLDIGTNSVGWA VITDEYKVPSKKFKVLGNTDRHSIKKNLIG ALLFDSGETAEATRLKRTARRRYTRRKNRI CYLQEIFSNEMAKVDDSFFHRLEESFLVEE DKKHERHPIFGNIVDEVAYHEKYPTIYHLR KKLVDSTDKADLRLIYLALAHMIKFRGHFL IEGDLNPDNSDVDKLFIQLVQTYNQLFEEN PINASGVDAKAILSARLSKSRRLENLIAQL PGEKKNGLFGNLIALSLGLTPNFKSNFDLA EDAKLQLSKDTYDDDDNLLAQIGDQYADLF LAAKNLSDAILLSDILRVNTEITKAPLSAS MIKRYDEHHQDLTLLKALVRQQLPEKYKEI FFDQSKNGYAGYIDGGASQEEFYKFIKPIL EKMDGTEELLVKLNREDLLRKQRTFDNGSI PHQIHLGELHAILRRQEDFYPFLKDNREKI EKILTFRIPYYVGPLARGNSRFAWMTRKSE ETITPWNFEEVVDKGASAQSFIERMTNFDK NLPNEKVLPKHSLLYEYFTVYNELTKVKYV TEGMRKPAFLSGEQKKAIVDLLFKTNRKVT VKQLKEDYFKKIECFDSVEISGVEDRFNAS LGTYHDLLKIIKDKDFLDNEENEDILEDIV LTLTLFEDREMIEERLKTYAHLFDDKVMKQ LKRRRYTGWGRLSRKLINGIRDKQSGKTIL DFLKSDGFANRNFMQLIHDDSLTFKEDIQK AQVSGQGDSLHEHIANLAGSPAIKKGILQT VKVVDELVKVMGRHKPENIVIEMARENQTT QKGQKNSRERMKRIEEGIKELGSQILKEHP VENTQLQNEKLYLYYLQNGRDMYVDQELDI NRLSDYDVDHIVPQSFLKDDSIDNKVLTRS DKARGKSDNVPSEEVVKKMKNYWRQLLNAK LITQRKFDNLTKAERGGLSELDKAGFIKRQ LVETRQITKHVAQILDSRMNTKYDENDKLI REVKVITLKSKLVSDFRKDFQFYKVREINN YHHAHDAYLNAVVGTALIKKYPKLESEFVY GDYKVYDVRKMIAKSEQEIGKATAKYFFYS NIMNFFKTEITLANGEIRKRPLIETNGETG EIVWDKGRDFATVRKVLSMPQVNIVKKTEV QTGGFSKESILPKRNSDKLIARKKDWDPKK YGGFDSPTVAYSVLVVAKVEKGKSKKLKSV KELLGITIMERSSFEKNPIDFLEAKGYKEV KKDLIIKLPKYSLFELENGRKRMLASAGEL QKGNELALPSKYVNFLYLASHYEKLKGSPE DNEQKQLFVEQHKHYLDEIIEQISEFSKRV ILADANLDKVLSAYNKHRDKPIREQAENII HLFTLTNLGAPAAFKYFDTTIDRKRYTSTK EVLDATLIHQSITGLYETRIDLSQLGGDGG AEAAAKEAAAKEAAAKEAAAKALEAEAAAK EAAAKEAAAKEAAAKAGGMDPLQLLQPLEA EIKGTKLKAHWNSGATITCVPQAFLEEEVP IKNIWIKTIHGEKEQPVYYLTFKIQGRKVE AEVISSPYDYILVSPSDIPWLMKKPLQLTT LVPLQEYEERLLKQTMLTGSYKEKLQSLFL KYDALWQHWENQVGHRRIKPHHIATGTVNP RPQKQYPINPKAKASIQTVINDLLKQGVLI QQNSIMNTPVYPVPKPDGKWRMVLDYREVN KTIPLIAAQNQHSAGILSSIFRGKYKTTLD LSNGFWAHSITPESYWLTAFTWLGQQYCWT RLPQGFLNSPALFNADVVDLLKEVPNVQVY VDDIYISHDDPREHLEQLEKVFSLLLNAGY VVSLKKSEIAQHEVEFLGFNITKEGRGLTE TFKQKLLNITPPRDLKQLQSILGKLNFARN FIPNFSELVKPLYNIIATAPGKYITWTTDN SQQLQNIISMLNSAENLEERNPEVRLIMKV NTSPSAGYIRFYNEFAKRPIMYLNYVYTKA EVKFTNTEKLLTTIHKGLIKALDLGMGQEI LVYSPIVSMTKIQKTPLPERKALPIRWITW MSYLEDPRIQFHYDKTLPELQQVPTVTDDI IAKIKHPSEFSMVFYTDGSAIKHPNVNKSH NAGMGIAQVQFKPEFTVINTWSIPLGDHTA QLAEVAAVEFACKKALKIDGPVLIVTDSFY VAESVNKELPYWQSNGFFNNKKKPLKHVSK WKSIADCIQLKPDIIIIHEKGHQPTASTFH TEGNNLADKLATQGSYVVNAGKRTADGSEF EKRTADGSEFESPKKKAKVE (SEQ ID NO: 11,094)

U2OS cells comprising a BFP landing pad (as described in Example 1 for HEK293T cells) were nucleofected with mRNA encoding one of the exemplary gene modifying polypeptides along with a template RNA designed to convert BFP to GFP, as described herein (FIG. 12A). The relative amounts of GFP positive cells (successfully edited) and BFP positive cells (unedited cells) were determined by flow cytometry and used to determine the editing activities of the gene modifying polypeptides in this experimental system. The results showed that all four exemplary gene modifying polypeptides showed high editing activity (from about 60% to over 85%).

U2OS cells were nucleofected with mRNA encoding one of the exemplary gene modifying polypeptides along with a template RNA designed to edit the HEK3 locus and a second strand-targeting gRNA (FIG. 12B). Editing was confirmed by amplicon sequencing using primers specific for the target locus. The results showed that all four exemplary gene modifying polypeptides showed editing activity at the HEK3 locus (from about 1% to about 5%).

Primary murine hepatocytes were nucleofected with mRNA encoding one of the exemplary gene modifying polypeptides along with a second strand-targeting gRNA and a template RNA designed to convert a G nucleotide to an A nucleotide in the endogenous Fah locus in wildtype mouse primary hepatocytes (FIG. 12C). A mutation in the last nucleotide of exon 8 of the Fah gene leads to aberrant mRNA splicing and subsequent mRNA degradation, without the production of Fah protein and, and thus serves as a mouse model of hereditary tyrosinemia type I; editing said nucleotide from G to A demonstrates the ability of a gene modifying system to target the mouse model's relevant locus. Editing was confirmed by amplicon sequencing using primers specific for the murine Fah target locus. The results showed that three of the four exemplary gene modifying polypeptides showed editing activity at the murine Fah locus (from about 6% to about 9%).

The gene modifying system comprising mRNA encoding one of the exemplary gene modifying polypeptides and a template RNA were formulated in LNP and delivered to Fah5981SB mice (FIG. 12D). The template RNA was designed to convert an A nucleotide to a G nucleotide in the Fah5981SB mouse model into the endogenous Fah locus in mouse liver. The Fah5981SB mouse model harbors a G to A point mutation in the last nucleotide of exon 8 of the Fah gene, leading to aberrant mRNA splicing and subsequent mRNA degradation, without the production of Fah protein and serves as a mouse model of hereditary tyrosinemia type I. Specifically, 2 mg/kg of total RNA equivalent formulated in LNPs, combined at 1:1 (w/w) of template RNA and mRNA, were dosed intravenously in 7 to 9-week-old, mixed gender Fah5981SB mice. 6 days post-dosing animals were sacrificed, and their liver collected for analyses. To analyze gene editing activity, primers flanking the target insertion site locus were used to amplify across the locus in the genomic DNA of liver samples collected 6 days post-dosing. Amplicons were analyzed via short read sequencing using an Illumina MiSeq. Conversion of an A nucleotide to a G nucleotide indicates successful editing. Results showed that three of the four exemplary gene modifying polypeptides showed editing activity in vivo in murine liver (from about 1.2% to about 6%).

Taken together, FIGS. 12A-12D show that the RNA delivery of several exemplary gene modifying polypeptides can achieve significant editing activity across different target loci, in different cell types, and in vivo at a therapeutically relevant locus. Additionally, the results further demonstrate that exemplary gene modifying polypeptides comprising a

(SEQ ID NO: 11,041) AEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKEAAAKA linker, shown in Example 5 to be particularly effective in gene modifying polypeptides, can be used to achieve significant editing activity across different target loci, in different cell types, and in vivo at a therapeutically relevant locus. Additionally, the results further demonstrate that exemplary gene modifying polypeptides comprising RT domains from the SSFV, MMLV, AVIRE, or SSV RT families can achieve editing activity across different target loci, in different cell types, and in vivo at a therapeutically relevant locus.

Example 7: Characterizing the Editing Activity of 39 High Performing Exemplary Gene Modifying Polypeptides

This example describes characterization of the editing activity of a selection of 39 exemplary gene modifying polypeptides chosen from those identified in the preceding Examples based on their performance in the pooled RT family experiments. As described above, each gene modifying polypeptide contains Cas9 linked to a reverse transcriptase (RT). Specifically, this example describes the introduction of a gene modifying polypeptide to mammalian cells via lentiviral transduction, such that the RNA encoding the gene modifying polypeptide is reverse transcribed, integrated into the genome, and stably expressed in the mammalian cells, followed by transfection of a template guide RNA for in vitro editing, as a means of evaluating the editing activity of the individual gene modifying polypeptide.

In this example, exemplary gene modifying polypeptides comprised the following combinations of linkers and RT domains fused to a Cas9 domain:

SEQ ID Graph ID Linker amino acid sequence NO: RT Variant Name 10373 PAPGGSGGG 11,051 MLVMS_P03355_PLV919 13642 GSSEAAAKGGG 11,052 MLVAV_P03356_3mutA 12793 EAAAKPAPGGS 11,053 MLVCB_P08361_3mutA 13522 GSSGGGEAAAK 11,054 MLVMS_P03355_3mutA_WS 16382 PAPGSSEAAAK 11,055 MLVMS_P03355_3mutA_WS 9438 GGGEAAAKGGS 11,056 XMRV6_A1Z651_3mutA 16661 AEAAAKEAAAKEAAAKEAAAKALEAE 11,057 MLVMS_P03355_PLV919 AAAKEAAAKEAAAKEAAAKA 5077 PAPAPAPAPAPAP 11,058 MLVFF_P26809_3mutA 14944 GGGEAAAKPAP 11,059 MLVFF_P26809_3mutA 15953 GSSPAPEAAAK 11,060 MLVMS_P03355_3mutA_WS 5082 PAPAPAPAPAPAP 11,061 MLVMS_P03355_PLV919 13233 GGGGSSEAAAK 11,062 MLVMS_P03355_PLV919 5071 PAPAPAPAPAPAP 11,063 MLVCB_P08361_3mutA 17380 SGGSSGGSSGSETPGTSESATPESSGGSSGGSS 11,064 MLVMS_P03355_PLV919 12507 GGSPAPEAAAK 11,065 MLVCB_P08361_3mutA 4213 EAAAKEAAAKEAAAKEAAAKEAAAKEAAAK 11,066 MLVCB_P08361_3mutA 12438 GGSEAAAKPAP 11,067 WMSV_P03359_3mutA 16591 AEAAAKEAAAKEAAAKEAAAKALE 11,068 AVIRE_P03360_3mutA AEAAAKEAAAKEAAAKEAAAKA 3927 EAAAKEAAAKEAAAKEAAAK 11,069 MLVCB_P08361_3mutA 16664 AEAAAKEAAAKEAAAKEAAAKAL 11,070 MLVMS_P03355_3mutA_WS EAEAAAKEAAAKEAAAKEAAAKA 12807 EAAAKPAPGGS 11,071 MLVMS_P03355_3mutA_WS 1576 GGGGSGGGGSGGGGSGGGGSGGGGSGGGGS 11,072 AVIRE_P03360_3mutA 1646 GGGGSGGGGSGGGGSGGGGSGGGGSGGGGS 11,073 MLVMS_P03355_PLV919 14586 GSSPAPGGG 11,074 XMRV6_A1Z651_3mutA 14652 PAPGGGGSS 11,075 MLVCB_P08361_3mutA 1353 GGGGSGGGGSGGGGSGGGGS 11,076 MLVCB_P08361_3mutA 9370 GGGEAAAKGGS 11,077 MLVMS_P03355_3mut 6831 EAAAKGGG 11,078 PERV_Q4VFZ2_3mut 12513 GGSPAPEAAAK 11,079 MLVFF_P26809_3mutA 15021 GGGPAPEAAAK 11,080 BAEVM_P10272_3mutA 8576 GGGGSSGGS 11,081 WMSV_P03359_3mut 16609 AEAAAKEAAAKEAAAKEAAAKAL 11,082 FLV_P10273_3mutA EAEAAAKEAAAKEAAAKEAAAKA 12691 EAAAKGGSPAP 11,083 PERV_Q4VFZ2_3mut 15894 GSSPAPEAAAK 11,084 FLV_P10273_3mutA 14924 GGGEAAAKPAP 11,085 KORV_Q9TTC1-Pro_3mutA 16704 AEAAAKEAAAKEAAAKEAAAKALE 11,086 SFV1_P23074_2mutA AEAAAKEAAAKEAAAKEAAAKA 4925 PAPAPAPAPAP 11,087 MLVBM_Q7SVK7_3mut 11771 GSSGGSPAP 11,088 HTLV2_P03363 707 GGSGGSGGSGGSGGS 11,089 WDSV_092815

The exemplary gene modifying polypeptides were introduced to HEK293T cells carrying a BFP-expressing genomic landing pad by transfection of mRNA. To determine the editing activity of the gene modifying polypeptide, BFP-expressing cells containing the gene modifying polypeptide—are electroporated with a template RNA designed to convert BFP-to-GFP. Cells were analyzed using flow cytometry for expression of the color-converted fluorescent protein 3-4 days post electroporation.

FIG. 13 shows a graph of the editing activity for the 39 exemplary gene modifying polypeptides when delivered to HEK293T cells in DNA (plasmid) form or RNA (mRNA) form along with an exemplary template RNA. The results showed that a gene modifying polypeptide can be delivered to cells in the form of mRNA and achieve comparable editing activity as the same gene modifying polypeptide delivered to cells in the form of DNA. Additionally, these results demonstrate that the gene modifying systems described herein can be delivered entirely in RNA form (e.g., via mRNA encoding the gene modifying polypeptide and a template RNA).

Example 8: Arrayed Screening of Individual Gene Modifying Polypeptides in HEK293T and U2OS Cells

This example describes identification and characterization of several classes of gene modifying polypeptides capable of editing genomic DNA.

HEK293T cells or U2OS cells expressing BFP (as described in preceding Examples) were nucleofected with a plasmid expressing one of 373 gene modifying polypeptides and a plasmid expressing either exemplary tgRNA g4 or exemplary tgRNA g10 (each designed to convert BFP to GFP) on day 0, and then flow cytometry was used to analyze BFP and GFP expression on day 4 (FIG. 15 ). Cells having GFP signal were defined as having undergone a successful rewriting event, and the percent of cells that were GFP+ on day 4 was used to determined the performance of each gene modifying polypeptide.

The percent converted to GFP for each gene modifying polypeptide and condition, normalized to PL12162 were graphed in a box and whisker plot (FIG. 16 ). The results confirm that the tested gene modifying polypeptides have editing activity. The results further demonstrate that a number of gene modifying polypeptides exhibit higher editing activity across the four conditions tested than the benchmark gene modifying polypeptide (showing a normalized percent converted greater than 1). Gene modifying polypeptides exhibiting higher editing activity than the benchmark gene modifying polypeptide in at least one condition or in all four conditions are listed in the following Tables, along with controls.

TABLE D11 Gene Modifying Polypeptides Exhibiting Higher Editing Activity Than Benchmark in at Least One Condition SEQ ID NOs 36 1384 2326 2644 2877 39 1390 2327 2647 2878 43 1401 2328 2648 2879 49 1404 2329 2653 2883 140 1405 2335 2677 2894 193 1406 2338 2688 2943 300 1618 2346 2692 2950 307 1672 2363 2711 3036 309 1857 2364 2712 3042 317 1861 2365 2713 3042 324 1864 2370 2734 3044 480 1865 2371 2776 3045 590 1870 2449 2780 3047 647 1883 2503 2781 3055 715 1943 2505 2782 3056 801 2087 2506 2784 3057 871 2089 2507 2788 3061 873 2091 2510 2790 3062 901 2097 2511 2793 3063 912 2099 2514 2794 3064 958 2101 2515 2795 3080 1006 2106 2518 2798 3081 1012 2115 2519 2803 3084 1017 2120 2525 2804 3086 1018 2300 2526 2809 3093 1038 2301 2527 2812 3094 1049 2303 2528 2817 7735 1171 2304 2534 2831 1197 2305 2542 2839 1198 2308 2610 2845 1225 2309 2611 2849 1371 2311 2614 2852 1372 2314 2615 2855 1373 2315 2619 2860 1374 2316 2623 2863 1376 2317 2624 2868 1377 2319 2633 2869 1380 2322 2636 2872 1382 2325 2641 2874

TABLE D12 Gene Modifying Polypeptides Exhibiting Higher Editing Activity Than Benchmark in All Conditions SEQ ID NOs 1018 1038 2309 2315 2325 2338 2611 2868 3084 7735

TABLE D13 Control sequences Normal- ization Positive Control Controls Negative Controls 2892 2181 MPAAKRVKLDGGDKKYSIGLDIGTNSVGWA VITDEYKVPSKKFKVLGNTDRHSIKKNLIG ALLFDSGETAEATRLKRTARRRYTRRKNRI CYLQEIFSNEMAKVDDSFFHRLEESFLVEE DKKHERHPIFGNIVDEVAYHEKYPTIYHLR KKLVDSTDKADLRLIYLALAHMIKFRGHFL IEGDLNPDNSDVDKLFIQLVQTYNQLFEEN PINASGVDAKAILSARLSKSRRLENLIAQL PGEKKNGLFGNLIALSLGLTPNFKSNFDLA EDAKLQLSKDTYDDDLDNLLAQIGDQYADL FLAAKNLSDAILLSDILRVNTEITKAPLSA SMIKRYDEHHQDLTLLKALVRQQLPEKYKE IFFDQSKNGYAGYIDGGASQEEFYKFIKPI LEKMDGTEELLVKLNREDLLRKQRTFDNGS IPHQIHLGELHAILRRQEDFYPFLKDNREK IEKILTFRIPYYVGPLARGNSRFAWMTRKS EETITPWNFEEVVDKGASAQSFIERMTNFD KNLPNEKVLPKHSLLYEYFTVYNELTKVKY VTEGMRKPAFLSGEQKKAIVDLLFKTNRKV TVKQLKEDYFKKIECFDSVEISGVEDRFNA SLGTYHDLLKIIKDKDFLDNEENEDILEDI VLTLTLFEDREMIEERLKTYAHLFDDKVMK QLKRRRYTGWGRLSRKLINGIRDKQSGKTI LDFLKSDGFANRNFMQLIHDDSLTFKEDIQ KAQVSGQGDSLHEHIANLAGSPAIKKGILQ TVKVVDELVKVMGRHKPENIVIEMARENQT TQKGQKNSRERMKRIEEGIKELGSQILKEH PVENTQLQNEKLYLYYLQNGRDMYVDQELD INRLSDYDVDHIVPQSFLKDDSIDNKVLTR SDKARGKSDNVPSEEVVKKMKNYWRQLLNA KLITQRKFDNLTKAERGGLSELDKAGFIKR QLVETRQITKHVAQILDSRMNTKYDENDKL IREVKVITLKSKLVSDFRKDFQFYKVREIN NYHHAHDAYLNAVVGTALIKKYPKLESEFV YGDYKVYDVRKMIAKSEQEIGKATAKYFFY SNIMNFFKTEITLANGEIRKRPLIETNGET GEIVWDKGRDFATVRKVLSMPQVNIVKKTE VQTGGFSKESILPKRNSDKLIARKKDWDPK KYGGFDSPTVAYSVLVVAKVEKGKSKKLKS VKELLGITIMERSSFEKNPIDFLEAKGYKE VKKDLIIKLPKYSLFELENGRKRMLASAGE LQKGNELALPSKYVNFLYLASHYEKLKGSP EDNEQKQLFVEQHKHYLDEIIEQISEFSKR VILADANLDKVLSAYNKHRDKPIREQAENI IHLFTLTNLGAPAAFKYFDTTIDRKRYTST KEVLDATLIHQSITGLYETRIDLSQLGGDG GGGSGGSGGSGGSGGSGGSCQTKNTLNIDE YLLQFPDQLWASLPTDIGRMLVPPITIKIK DNASLPSIRQYPLPKDKTEGLRPLISSLEN QGILIKCHSPCNTPIFPIKKAGRDEYRMIH DLRAINNIVAPLTAVVASPTTVLSNLAPSL HWFTVIDLSNAFFSVPIHKDSQYLFAFTFE GHQYTWTVLPQGFIHSPTLFSQALYQSLHK IKFKISSEICIYMDDVLIASKDRDTNLKDT AVMLQHLASEGHKVSKKKLQLCQQEVVYLG QLLTPEGRKILPDRKVTVSQFQQPTTIRQI RAFLGLVGYCRHWIPEFSIHSKFLEKQLKK DTAEPFQLDDQQVEAFNKLKHAITTAPVLV VPDPAKPFQLYTSHSEHASIAVLTQKHAGR TRPIAFLSSKFDAIESGLPPCLKACASIHR SLTQADSFILGAPLIIYTTHAICTLLQRDR SQLVTASRFSKWEADLLRPELTFVACSAVS PAHLYMQSCENNIPPHDCVLLTHTISRPRP DLSDLPIPDPDMTLFSDGSYTTGRGGAAVV MHRPVTDDFIIIHQQPGGASAQTAELLALA AACHLATDKTVNIYTDSRYAYGVVHDFGHL WMHRGFVTSAGTPIKNHKEIEYLLKQIMKP KQVSVIKIEAHTKGVSMEVRGNAAADEAAK NAVFLVQRAGKRTADGSEFEKRTADGSEFE SPKKKAKVE (SEQ ID NO: 15466) 3143 MPAAKRVKLDGGDKKYSIGLDIGTNSVGWA VITDEYKVPSKKFKVLGNTDRHSIKKNLIG ALLFDSGETAEATRLKRTARRRYTRRKNRI CYLQEIFSNEMAKVDDSFFHRLEESFLVEE DKKHERHPIFGNIVDEVAYHEKYPTIYHLR KKLVDSTDKADLRLIYLALAHMIKFRGHFL IEGDLNPDNSDVDKLFIQLVQTYNQLFEEN PINASGVDAKAILSARLSKSRRLENLIAQL PGEKKNGLFGNLIALSLGLTPNFKSNFDLA EDAKLQLSKDTYDDDLDNLLAQIGDQYADL FLAAKNLSDAILLSDILRVNTEITKAPLSA SMIKRYDEHHQDLTLLKALVRQQLPEKYKE IFFDQSKNGYAGYIDGGASQEEFYKFIKPI LEKMDGTEELLVKLNREDLLRKQRTFDNGS IPHQIHLGELHAILRRQEDFYPFLKDNREK IEKILTFRIPYYVGPLARGNSRFAWMTRKS EETITPWNFEEVVDKGASAQSFIERMTNFD KNLPNEKVLPKHSLLYEYFTVYNELTKVKY VTEGMRKPAFLSGEQKKAIVDLLFKTNRKV TVKQLKEDYFKKIECFDSVEISGVEDRFNA SLGTYHDLLKIIKDKDFLDNEENEDILEDI VLTLTLFEDREMIEERLKTYAHLFDDKVMK QLKRRRYTGWGRLSRKLINGIRDKQSGKTI LDFLKSDGFANRNFMQLIHDDSLTFKEDIQ KAQVSGQGDSLHEHIANLAGSPAIKKGILQ TVKVVDELVKVMGRHKPENIVIEMARENQT TQKGQKNSRERMKRIEEGIKELGSQILKEH PVENTQLQNEKLYLYYLQNGRDMYVDQELD INRLSDYDVDHIVPQSFLKDDSIDNKVLTR SDKARGKSDNVPSEEVVKKMKNYWRQLLNA KLITQRKFDNLTKAERGGLSELDKAGFIKR QLVETRQITKHVAQILDSRMNTKYDENDKL IREVKVITLKSKLVSDFRKDFQFYKVREIN NYHHAHDAYLNAVVGTALIKKYPKLESEFV YGDYKVYDVRKMIAKSEQEIGKATAKYFFY SNIMNFFKTEITLANGEIRKRPLIETNGET GEIVWDKGRDFATVRKVLSMPQVNIVKKTE VQTGGFSKESILPKRNSDKLIARKKDWDPK KYGGFDSPTVAYSVLVVAKVEKGKSKKLKS VKELLGITIMERSSFEKNPIDFLEAKGYKE VKKDLIIKLPKYSLFELENGRKRMLASAGE LQKGNELALPSKYVNFLYLASHYEKLKGSP EDNEQKQLFVEQHKHYLDEIIEQISEFSKR VILADANLDKVLSAYNKHRDKPIREQAENI IHLFTLTNLGAPAAFKYFDTTIDRKRYTST KEVLDATLIHQSITGLYETRIDLSQLGGDG GGSSGGSEAAAKGGSCQTKNTLNIDEYLLQ FPDQLWASLPTDIGRMLVPPITIKIKDNAS LPSIRQYPLPKDKTEGLRPLISSLENQGIL IKCHSPCNTPIFPIKKAGRDEYRMIHDLRA INNIVAPLTAVVASPTTVLSNLAPSLHWFT VIDLSNAFFSVPIHKDSQYLFAFTFEGHQY TWTVLPQGFIHSPTLFNQALYQSLHKIKFK ISSEICIYMDDVLIASKDRDTNLKDTAVML QHLASEGHKVSKKKLQLCQQEVVYLGQLLT PEGRKILPDRKVTVSQFQQPTTIRQIRAFL GKVGYCRHFIPEFSIHSKFLEKQLKPDTAE PFQLDDQQVEAFNKLKHAITTAPVLVVPDP AKPFQLYTSHSEHASIAVLTQKHAGRTRPI AFLSSKFDAIESGLPPCLKACASIHRSLTQ ADSFILGAPLIIYTTHAICTLLQRDRSQLV TASRFSKWEADLLRPELTFVACSAVSPAHL YMQSCENNIPPHDCVLLTHTISRPRPDLSD LPIPDPDMTLFSDGSYTTGRGGAAVVMHRP VTDDFIIIHQQPGGASAQTAELLALAAACH LATDKTVNIYTDSRYAYGVVHDFGHLWMHR GFVTSAGTPIKNHKEIEYLLKQIMKPKQVS VIKIEAHTKGVSMEVRGNAAADEAAKNAVF LVQRAGKRTADGSEFEKRTADGSEFESPKK KAKVE (SEQ ID NO: 15467) MPAAKRVKLDGGDKKYSIGLDIGTNSVGWA VITDEYKVPSKKFKVLGNTDRHSIKKNLIG ALLFDSGETAEATRLKRTARRRYTRRKNRI CYLQEIFSNEMAKVDDSFFHRLEESFLVEE DKKHERHPIFGNIVDEVAYHEKYPTIYHLR KKLVDSTDKADLRLIYLALAHMIKFRGHFL IEGDLNPDNSDVDKLFIQLVQTYNQLFEEN PINASGVDAKAILSARLSKSRRLENLIAQL PGEKKNGLFGNLIALSLGLTPNFKSNFDLA EDAKLQLSKDTYDDDLDNLLAQIGDQYADL FLAAKNLSDAILLSDILRVNTEITKAPLSA SMIKRYDEHHQDLTLLKALVRQQLPEKYKE IFFDQSKNGYAGYIDGGASQEEFYKFIKPI LEKMDGTEELLVKLNREDLLRKQRTFDNGS IPHQIHLGELHAILRRQEDFYPFLKDNREK IEKILTFRIPYYVGPLARGNSRFAWMTRKS EETITPWNFEEVVDKGASAQSFIERMTNFD KNLPNEKVLPKHSLLYEYFTVYNELTKVKY VTEGMRKPAFLSGEQKKAIVDLLFKTNRKV TVKQLKEDYFKKIECFDSVEISGVEDRFNA SLGTYHDLLKIIKDKDFLDNEENEDILEDI VLTLTLFEDREMIEERLKTYAHLFDDKVMK QLKRRRYTGWGRLSRKLINGIRDKQSGKTI LDFLKSDGFANRNFMQLIHDDSLTFKEDIQ KAQVSGQGDSLHEHIANLAGSPAIKKGILQ TVKVVDELVKVMGRHKPENIVIEMARENQT TQKGQKNSRERMKRIEEGIKELGSQILKEH PVENTQLQNEKLYLYYLQNGRDMYVDQELD INRLSDYDVDHIVPQSFLKDDSIDNKVLTR SDKARGKSDNVPSEEVVKKMKNYWRQLLNA KLITQRKFDNLTKAERGGLSELDKAGFIKR QLVETRQITKHVAQILDSRMNTKYDENDKL IREVKVITLKSKLVSDFRKDFQFYKVREIN NYHHAHDAYLNAVVGTALIKKYPKLESEFV YGDYKVYDVRKMIAKSEQEIGKATAKYFFY SNIMNFFKTEITLANGEIRKRPLIETNGET GEIVWDKGRDFATVRKVLSMPQVNIVKKTE VQTGGFSKESILPKRNSDKLIARKKDWDPK KYGGFDSPTVAYSVLVVAKVEKGKSKKLKS VKELLGITIMERSSFEKNPIDFLEAKGYKE VKKDLIIKLPKYSLFELENGRKRMLASAGE LQKGNELALPSKYVNFLYLASHYEKLKGSP EDNEQKQLFVEQHKHYLDEIIEQISEFSKR VILADANLDKVLSAYNKHRDKPIREQAENI IHLFTLTNLGAPAAFKYFDTTIDRKRYTST KEVLDATLIHQSITGLYETRIDLSQLGGDG GGSSGGSPAPGGHLPPPPQVDQFPLNLPER LQALNDLVSKALEAGHIEPYSGPGNNPVFP VKKPNGKWRFIHDLRATNAITTTLTSPSPG PPDLTSLPTALPHLQTIDLTDAFFQIPLPK QYQPYFAFTIPQPCNYGPGTRYAWTVLPQG FKNSPTLFEQQLAAVLNPMRKMFPTSTIVQ YMDDILLASPTNEELQQLSQLTLQALTTHG LPISQEKTQQTPGQIRFLGQVISPNHITYE STPTIPIKSQWTLTELQVILGEIQWVSKGT PILRKHLQSLYSALHGYRDPRACITLTPQQ LHALHAIQQALQHNCRGRLNPALPLLGLIS LSTSGTTSVIFQPKQNWPLAWLHTPHPPTS LCPWGHLLACTILTLDKYTLQHYGQLCQSF HHNMSKQALCDFLRNSPHPSVGILIHHMGR FHNLGSQPSGPWKTLLHLPTLLQEPRLLRP IFTLSPVVLDTAPCLFSDGSPQKAAYVLWD QTILQQDITPLPSHETHSAQKGELLALICG LRAAKPWPSLNIFLDSKYLIKYLHSLAIGA FLGTSAHQTLQAALPPLLQGKTIYLHHVRS HTNLPDPISTFNEYTDSLILAPLVPLAGKR TADGSEFEKRTADGSEFESPKKKAKVE (SEQ ID NO: 15468) MPAAKRVKLDGGDKKYSIGLDIGTNSVGWA VITDEYKVPSKKFKVLGNTDRHSIKKNLIG ALLFDSGETAEATRLKRTARRRYTRRKNRI CYLQEIFSNEMAKVDDSFFHRLEESFLVEE DKKHERHPIFGNIVDEVAYHEKYPTIYHLR KKLVDSTDKADLRLIYLALAHMIKFRGHFL IEGDLNPDNSDVDKLFIQLVQTYNQLFEEN PINASGVDAKAILSARLSKSRRLENLIAQL PGEKKNGLFGNLIALSLGLTPNFKSNFDLA EDAKLQLSKDTYDDDLDNLLAQIGDQYADL FLAAKNLSDAILLSDILRVNTEITKAPLSA SMIKRYDEHHQDLTLLKALVRQQLPEKYKE IFFDQSKNGYAGYIDGGASQEEFYKFIKPI LEKMDGTEELLVKLNREDLLRKQRTFDNGS IPHQIHLGELHAILRRQEDFYPFLKDNREK IEKILTFRIPYYVGPLARGNSRFAWMTRKS EETITPWNFEEVVDKGASAQSFIERMTNFD KNLPNEKVLPKHSLLYEYFTVYNELTKVKY VTEGMRKPAFLSGEQKKAIVDLLFKTNRKV TVKQLKEDYFKKIECFDSVEISGVEDRFNA SLGTYHDLLKIIKDKDFLDNEENEDILEDI VLTLTLFEDREMIEERLKTYAHLFDDKVMK QLKRRRYTGWGRLSRKLINGIRDKQSGKTI LDFLKSDGFANRNFMQLIHDDSLTFKEDIQ KAQVSGQGDSLHEHIANLAGSPAIKKGILQ TVKVVDELVKVMGRHKPENIVIEMARENQT TQKGQKNSRERMKRIEEGIKELGSQILKEH PVENTQLQNEKLYLYYLQNGRDMYVDQELD INRLSDYDVDHIVPQSFLKDDSIDNKVLTR SDKARGKSDNVPSEEVVKKMKNYWRQLLNA KLITQRKFDNLTKAERGGLSELDKAGFIKR QLVETRQITKHVAQILDSRMNTKYDENDKL IREVKVITLKSKLVSDFRKDFQFYKVREIN NYHHAHDAYLNAVVGTALIKKYPKLESEFV YGDYKVYDVRKMIAKSEQEIGKATAKYFFY SNIMNFFKTEITLANGEIRKRPLIETNGET GEIVWDKGRDFATVRKVLSMPQVNIVKKTE VQTGGFSKESILPKRNSDKLIARKKDWDPK KYGGFDSPTVAYSVLVVAKVEKGKSKKLKS VKELLGITIMERSSFEKNPIDFLEAKGYKE VKKDLIIKLPKYSLFELENGRKRMLASAGE LQKGNELALPSKYVNFLYLASHYEKLKGSP EDNEQKQLFVEQHKHYLDEIIEQISEFSKR VILADANLDKVLSAYNKHRDKPIREQAENI IHLFTLTNLGAPAAFKYFDTTIDRKRYTST KEVLDATLIHQSITGLYETRIDLSQLGGDG GGSSGGSPAPGGSCQTKNTLNIDEYLLQFP DQLWASLPTDIGRMLVPPITIKIKDNASLP SIRQYPLPKDKTEGLRPLISSLENQGILIK CHSPCNTPIFPIKKAGRDEYRMIHDLRAIN NIVAPLTAVVASPTTVLSNLAPSLHWFTVI DLSNAFFSVPIHKDSQYLFAFTFEGHQYTW TVLPQGFIHSPTLFNQALYQSLHKIKFKIS SEICIYMDDVLIASKDRDTNLKDTAVMLQH LASEGHKVSKKKLQLCQQEVVYLGQLLTPE GRKILPDRKVTVSQFQQPTTIRQIRAFLGK VGYCRHFIPEFSIHSKFLEKQLKPDTAEPF QLDDQQVEAFNKLKHAITTAPVLVVPDPAK PFQLYTSHSEHASIAVLTQKHAGRTRPIAF LSSKFDAIESGLPPCLKACASIHRSLTQAD SFILGAPLIIYTTHAICTLLQRDRSQLVTA SRFSKWEADLLRPELTFVACSAVSPAHLYM QSCENNIPPHDCVLLTHTISRPRPDLSDLP IPDPDMTLFSDGSYTTGRGGAAVVMHRPVT DDFIIIHQQPGGASAQTAELLALAAACHLA TDKTVNIYTDSRYAYGVVHDFGHLWMHRGF VTSAGTPIKNHKEIEYLLKQIMKPKQVSVI KIEAHTKGVSMEVRGNAAADEAAKNAVFLV QRAGKRTADGSEFEKRTADGSEFESPKKKA KVE(SEQ ID NO: 15469) MPAAKRVKLDGGDKKYSIGLDIGTNSVGWA VITDEYKVPSKKFKVLGNTDRHSIKKNLIG ALLFDSGETAEATRLKRTARRRYTRRKNRI CYLQEIFSNEMAKVDDSFFHRLEESFLVEE DKKHERHPIFGNIVDEVAYHEKYPTIYHLR KKLVDSTDKADLRLIYLALAHMIKFRGHFL IEGDLNPDNSDVDKLFIQLVQTYNQLFEEN PINASGVDAKAILSARLSKSRRLENLIAQL PGEKKNGLFGNLIALSLGLTPNFKSNFDLA EDAKLQLSKDTYDDDLDNLLAQIGDQYADL FLAAKNLSDAILLSDILRVNTEITKAPLSA SMIKRYDEHHQDLTLLKALVRQQLPEKYKE IFFDQSKNGYAGYIDGGASQEEFYKFIKPI LEKMDGTEELLVKLNREDLLRKQRTFDNGS IPHQIHLGELHAILRRQEDFYPFLKDNREK IEKILTFRIPYYVGPLARGNSRFAWMTRKS EETITPWNFEEVVDKGASAQSFIERMTNFD KNLPNEKVLPKHSLLYEYFTVYNELTKVKY VTEGMRKPAFLSGEQKKAIVDLLFKTNRKV TVKQLKEDYFKKIECFDSVEISGVEDRFNA SLGTYHDLLKIIKDKDFLDNEENEDILEDI VLTLTLFEDREMIEERLKTYAHLFDDKVMK QLKRRRYTGWGRLSRKLINGIRDKQSGKTI LDFLKSDGFANRNFMQLIHDDSLTFKEDIQ KAQVSGQGDSLHEHIANLAGSPAIKKGILQ TVKVVDELVKVMGRHKPENIVIEMARENQT TQKGQKNSRERMKRIEEGIKELGSQILKEH PVENTQLQNEKLYLYYLQNGRDMYVDQELD INRLSDYDVDHIVPQSFLKDDSIDNKVLTR SDKARGKSDNVPSEEVVKKMKNYWRQLLNA KLITQRKFDNLTKAERGGLSELDKAGFIKR QLVETRQITKHVAQILDSRMNTKYDENDKL IREVKVITLKSKLVSDFRKDFQFYKVREIN NYHHAHDAYLNAVVGTALIKKYPKLESEFV YGDYKVYDVRKMIAKSEQEIGKATAKYFFY SNIMNFFKTEITLANGEIRKRPLIETNGET GEIVWDKGRDFATVRKVLSMPQVNIVKKTE VQTGGFSKESILPKRNSDKLIARKKDWDPK KYGGFDSPTVAYSVLVVAKVEKGKSKKLKS VKELLGITIMERSSFEKNPIDFLEAKGYKE VKKDLIIKLPKYSLFELENGRKRMLASAGE LQKGNELALPSKYVNFLYLASHYEKLKGSP EDNEQKQLFVEQHKHYLDEIIEQISEFSKR VILADANLDKVLSAYNKHRDKPIREQAENI IHLFTLTNLGAPAAFKYFDTTIDRKRYTST KEVLDATLIHQSITGLYETRIDLSQLGGDG GGGGPAPGSSGGHLPPPPQVDQFPLNLPER LQALNDLVSKALEAGHIEPYSGPGNNPVFP VKKPNGKWRFIHDLRATNAITTTLTSPSPG PPDLTSLPTALPHLQTIDLTDAFFQIPLPK QYQPYFAFTIPQPCNYGPGTRYAWTVLPQG FKNSPTLFQQQLAAVLNPMRKMFPTSTIVQ YMDDILLASPTNEELQQLSQLTLQALTTHG LPISQEKTQQTPGQIRFLGQVISPNHITYE STPTIPIKSQWTLTELQVILGEIQWVSKGT PILRKHLQSLYSALHPYRDPRACITLTPQQ LHALHAIQQALQHNCRGRLNPALPLLGLIS LSTSGTTSVIFQPKQNWPLAWLHTPHPPTS LCPWGHLLACTILTLDKYTLQHYGQLCQSF HHNMSKQALCDFLRNSPHPSVGILIHHMGR FHNLGSQPSGPWKTLLHLPTLLQEPRLLRP IFTLSPVVLDTAPCLFSDGSPQKAAYVLWD QTILQQDITPLPSHETHSAQKGELLALICG LRAAKPWPSLNIFLDSKYLIKYLHSLAIGA FLGTSAHQTLQAALPPLLQGKTIYLHHVRS HTNLPDPISTFNEYTDSLILAPLVPLAGKR TADGSEFEKRTADGSEFESPKKKAKVE (SEQ ID NO: 15470)

The data from each candidate tested within an RT family were grouped and compared to the data for the pooled RT families tested in the preceding Examples to verify that the trends seen in the pooled experiments were replicated when the candidates were tested individually (FIG. 17 ). The results confirmed that the performance of exemplary gene modifying polypeptides when tested individually recapitulated the trends observed in the pooled experiments.

It should be understood that for all numerical bounds describing some parameter in this application, such as “about,” “at least,” “less than,” and “more than,” the description also necessarily encompasses any range bounded by the recited values. Accordingly, for example, the description “at least 1, 2, 3, 4, or 5” also describes, inter alia, the ranges 1-2, 1-3, 1-4, 1-5, 2-3, 2-4, 2-5, 3-4, 3-5, and 4-5, et cetera.

For all patents, applications, or other reference cited herein, such as non-patent literature and reference sequence information, it should be understood that they are incorporated by reference in their entirety for all purposes as well as for the proposition that is recited. Where any conflict exists between a document incorporated by reference and the present application, this application will control. All information associated with reference gene sequences disclosed in this application, such as GeneIDs or accession numbers (typically referencing NCBI accession numbers), including, for example, genomic loci, genomic sequences, functional annotations, allelic variants, and reference mRNA (including, e.g., exon boundaries or response elements) and protein sequences (such as conserved domain structures), as well as chemical references (e.g., PubChem compound, PubChem substance, or PubChem Bioassay entries, including the annotations therein, such as structures and assays, et cetera), are hereby incorporated by reference in their entirety.

Headings used in this application are for convenience only and do not affect the interpretation of this application.

LENGTHY TABLES The patent application contains a lengthy table section. A copy of the table is available in electronic form from the USPTO web site (https://seqdata.uspto.gov/?pageRequest=docDetail&DocID=US20240002886A1). An electronic copy of the table will also be available from the USPTO upon request and payment of the fee set forth in 37 CFR 1.19(b)(3). 

1. A gene modifying polypeptide comprising: a reverse transcriptase (RT) domain having the sequence of SEQ ID NO: 8,003; a Cas9 nickase domain, wherein the RT domain is C-terminal of the Cas9 nickase domain; and a linker disposed between the RT domain and the Cas9 nickase domain, wherein the linker comprises the sequence of SEQ ID NO: 15,401.
 2. The gene modifying polypeptide of claim 1, wherein the Cas9 nickase domain is a SpyCas9 nickase domain.
 3. The gene modifying polypeptide of claim 1, wherein the Cas9 nickase domain comprises an N863A mutation.
 4. The gene modifying polypeptide of claim 1, wherein the Cas9 nickase domain comprises an amino acid sequence of SEQ ID NO: 11,096.
 5. The gene modifying polypeptide of claim 1, wherein the Cas9 nickase domain is an NmeCas9 domain.
 6. The gene modifying polypeptide of claim 1, wherein the Cas9 nickase domain is an St1Cas9 domain.
 7. The gene modifying polypeptide of claim 1, wherein the Cas9 nickase domain is a SauCas9 domain.
 8. The gene modifying polypeptide of claim 1, which comprises a nuclear localization signal (NLS).
 9. The gene modifying polypeptide of claim 1, which comprises a first NLS which is N-terminal of the Cas9 nickase domain.
 10. The gene modifying polypeptide of claim 1, which comprises an NLS which is C-terminal of the RT domain.
 11. The gene modifying polypeptide of claim 1, which comprises a first NLS which is N-terminal of the Cas9 nickase domain and a second NLS which is C-terminal of the RT domain.
 12. The gene modifying polypeptide of claim 1, which comprises a first NLS which is N-terminal of the Cas9 nickase domain, wherein the first NLS comprises an amino acid sequence of PAAKRVKLD (SEQ ID NO: 11,095).
 13. The gene modifying polypeptide of claim 1, which comprises an NLS which is C-terminal of the RT domain and comprises an amino acid sequence of KRTADGSEFE (SEQ ID NO: 4650).
 14. The gene modifying polypeptide of claim 1, which comprises an NLS which is C-terminal of the RT domain and comprises an amino acid sequence of KRTADGSEFESPKKKAKVE (SEQ ID NO: 4651).
 15. The gene modifying polypeptide of claim 1, which comprises a sequence of SEQ ID NO: 4000 which comprises a first NLS and the Cas9 nickase domain.
 16. The gene modifying polypeptide of claim 1, which comprises an NLS having a sequence according to SEQ ID NO:
 4649. 17. The gene modifying polypeptide of claim 1, which comprises a GG amino acid sequence between the Cas9 nickase domain and the linker.
 18. The gene modifying polypeptide of claim 11, which comprises an AG amino acid sequence between the RT domain and the second NLS.
 19. The gene modifying polypeptide of claim 1, which comprises a GG amino acid sequence between the linker and the RT domain.
 20. The gene modifying polypeptide of claim 1, which comprises an amino acid sequence according to SEQ ID NO:
 1372. 21. A nucleic acid molecule encoding the gene modifying polypeptide of claim
 1. 22. The nucleic acid molecule of claim 21, which comprises RNA.
 23. A cell comprising: i) the gene modifying polypeptide of claim 1 or ii) a nucleic acid encoding the gene modifying polypeptide.
 24. A system comprising: i) the gene modifying polypeptide of claim 1, or a nucleic acid molecule encoding the gene modifying polypeptide, and ii) a template RNA that comprises: a) a gRNA spacer that is complementary to a portion of a target nucleic acid sequence; b) a gRNA scaffold that binds the Cas9 nickase domain of the gene modifying polypeptide; c) a heterologous object sequence; and d) a primer binding site sequence.
 25. A lipid nanoparticle formulation comprising the system of claim
 24. 26. A method for modifying a target nucleic acid molecule in a cell, the method comprising contacting the cell with the system of claim 24, thereby modifying the target nucleic acid molecule.
 27. A gene modifying polypeptide comprising: a reverse transcriptase (RT) domain having the sequence of Table 6; a Cas9 nickase domain, wherein the RT domain is C-terminal of the Cas9 nickase domain; and a linker disposed between the RT domain and the Cas9 nickase domain, wherein the linker comprises a sequence of Table 10, wherein if the RT domain has an amino acid sequence according to SEQ ID NO: 8,003, the linker does not have an amino acid sequence according to SEQ ID NO: 15,401.
 28. A composition comprising: a nucleic acid molecule encoding the gene modifying polypeptide of claim 27, a cell comprising the gene modifying polypeptide, or a cell comprising the nucleic acid encoding the gene modifying peptide.
 29. A system comprising: i) the gene modifying polypeptide of claim 27, or a nucleic acid molecule encoding the gene modifying polypeptide, and ii) a template RNA that comprises: a) a gRNA spacer that is complementary to a portion of a target nucleic acid sequence; b) a gRNA scaffold that binds the Cas9 nickase domain of the gene modifying polypeptide; c) a heterologous object sequence; and d) a primer binding site sequence.
 30. A method for modifying a target nucleic acid molecule in a cell, the method comprising contacting the cell with the system of claim 29, thereby modifying the target nucleic acid molecule. 